rs141281214

Variant names:

• chr12-21863055-C-T
• rs141281214
• NM_020297.4:c.2238-1G>A

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 2P and 9B. PVS1_Moderate BP6 BS1 BS2

The NM_020297.4(ABCC9):​c.2238-1G>A variant causes a splice acceptor, intron change. The variant allele was found at a frequency of 0.000759 in 1,588,992 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00076 (1 hom., cov: 32)
  • Exomes 𝑓: 0.00076 (8 hom.)
• Consequence: ABCC9 NM_020297.4 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:3 B:11
• Conservation: PhyloP100: 5.91
• Publications: 10 publications found

Genes affected

ABCC9 (HGNC:60): (ATP binding cassette subfamily C member 9) The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MRP subfamily which is involved in multi-drug resistance. This protein is thought to form ATP-sensitive potassium channels in cardiac, skeletal, and vascular and non-vascular smooth muscle. Protein structure suggests a role as the drug-binding channel-modulating subunit of the extra-pancreatic ATP-sensitive potassium channels. Mutations in this gene are associated with cardiomyopathy dilated type 1O. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2011]

ABCC9 Gene-Disease associations (from GenCC):

• hypertrichotic osteochondrodysplasia Cantu type

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
• dilated cardiomyopathy 1O

  Inheritance: AD Classification: STRONG, MODERATE, LIMITED Submitted by: Illumina, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• intellectual disability and myopathy syndrome

  Inheritance: AR Classification: MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• acromegaloid facial appearance syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• familial isolated dilated cardiomyopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• hypertrichosis-acromegaloid facial appearance syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Brugada syndrome

  Inheritance: AD Classification: LIMITED Submitted by: Genomics England PanelApp
• dilated cardiomyopathy

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• atrial fibrillation, familial, 12

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000257022 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -7 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.021935483 fraction of the gene. Cryptic splice site detected, with MaxEntScore 11, offset of 3, new splice context is: tctttttcatttttcaatAGgaa. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
• BP6: Variant 12-21863055-C-T is Benign according to our data. Variant chr12-21863055-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 162688.
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.000759 (108/142264) while in subpopulation SAS AF = 0.00548 (24/4382). AF 95% confidence interval is 0.00378. There are 1 homozygotes in GnomAd4. There are 56 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAdExome4 at 8 Unknown,AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCC9	NM_020297.4	c.2238-1G>A		splice_acceptor_variant, intron_variant	Intron 19 of 39	ENST00000261200.9	NP_064693.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCC9	ENST00000261200.9	c.2238-1G>A		splice_acceptor_variant, intron_variant	Intron 19 of 39	5	NM_020297.4	ENSP00000261200.4

Frequencies

GnomAD3 genomes AF: 0.000760 AC: 108 AN: 142160 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.0000792

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000221

Gnomad ASJ AF: 0.0151

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00547

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00333

Gnomad NFE AF: 0.000366

Gnomad OTH AF: 0.00156

GnomAD2 exomes AF: 0.00147 AC: 358 AN: 243104 AF XY: 0.00167

Gnomad AFR exome AF: 0.0000653

Gnomad AMR exome AF: 0.0000603

Gnomad ASJ exome AF: 0.0120

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000380

Gnomad OTH exome AF: 0.00103

GnomAD4 exome AF: 0.000759 AC: 1098 AN: 1446728 Hom.: 8 Cov.: 28 AF XY: 0.000899 AC XY: 648 AN XY: 720666

African (AFR) AF: 0.00 AC: 0 AN: 32948

American (AMR) AF: 0.0000226 AC: 1 AN: 44244

Ashkenazi Jewish (ASJ) AF: 0.0117 AC: 303 AN: 25920

East Asian (EAS) AF: 0.0000253 AC: 1 AN: 39560

South Asian (SAS) AF: 0.00546 AC: 468 AN: 85726

European-Finnish (FIN) AF: 0.0000188 AC: 1 AN: 53238

Middle Eastern (MID) AF: 0.00175 AC: 10 AN: 5708

European-Non Finnish (NFE) AF: 0.000198 AC: 218 AN: 1099604

Other (OTH) AF: 0.00161 AC: 96 AN: 59780

GnomAD4 genome AF: 0.000759 AC: 108 AN: 142264 Hom.: 1 Cov.: 32 AF XY: 0.000811 AC XY: 56 AN XY: 69026

African (AFR) AF: 0.0000789 AC: 3 AN: 38000

American (AMR) AF: 0.000221 AC: 3 AN: 13570

Ashkenazi Jewish (ASJ) AF: 0.0151 AC: 50 AN: 3320

East Asian (EAS) AF: 0.00 AC: 0 AN: 4804

South Asian (SAS) AF: 0.00548 AC: 24 AN: 4382

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9520

Middle Eastern (MID) AF: 0.00355 AC: 1 AN: 282

European-Non Finnish (NFE) AF: 0.000366 AC: 24 AN: 65586

Other (OTH) AF: 0.00155 AC: 3 AN: 1936

Alfa AF: 0.000785 Hom.: 4

Bravo AF: 0.000608

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000259 AC: 1

ESP6500AA AF: 0.000228 AC: 1

ESP6500EA AF: 0.00116 AC: 10

ExAC AF: 0.00158 AC: 192

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:3 Benign:11

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Benign:5

Apr 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ABCC9: BS2 -

Nov 27, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 26656175, 28166811, 23861362, 29030401, 28881617, 26046366, 30847666) -

-

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jun 24, 2013

Biesecker Lab/Clinical Genomics Section, National Institutes of Health

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: research

- -

not specified Uncertain:2 Benign:1

-

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 16, 2020

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: ABCC9 c.2238-1G>A is located in a canonical splice-site, which are typically predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. In the case of this variant, however, 4/4 computational tools predict that the variant abolishes a 3' acceptor site, but strengthens or creates a cryptic 3' acceptor site three bases downstream, which would be predicted to result in the deletion of only one amino acid from the protein. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0015 in 243104 control chromosomes in the gnomAD database, including 2 homozygotes. The observed variant frequency is approximately 59- fold the estimated maximal expected allele frequency for a pathogenic variant in ABCC9 causing Cardiomyopathy phenotype (2.5e-05), strongly suggesting that the variant is benign. c.2238-1G>A has been reported in the literature in individuals affected with Cardiomyopathy (examples- Bottillo_2016, Cirino_2017, Seidelmann_2017). These reports do not provide unequivocal conclusions about association of the variant with Cardiomyopathy. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. They cited the variant as benign (n=1), likley benign (n=2), and uncertain significance (n=2). Based on the evidence outlined above, the variant was classified as VUS-possibly benign. -

Mar 06, 2015

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant classified as Uncertain Significance - Favor Benign. The c.2238-1G>A var iant in ABCC9 has been identified by our laboratory in two individuals with DCM, one of whom carried a second pathogenic variant in another gene. It has also be en identified in 0.7% (118/16384) of South Asian chromosomes by the Exome Aggreg ation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs141281214). This frequency raises doubt as to whether this variant can cause a dominant disease. However, this variant is expected to abolish the 3? splice site of exon 18 and create a novel spice site 3 bases further downstream, which would result in an i n-frame deletion of one amino acid. In summary, additional information is needed to fully assess the clinical significance of the c.2238-1G>A variant. -

ABCC9-related disorder Uncertain:1 Benign:1

Oct 18, 2017

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

Oct 24, 2023

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Hypertrichotic osteochondrodysplasia Cantu type Benign:1

Mar 26, 2024

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dilated cardiomyopathy 1O Benign:1

Jan 30, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiomyopathy Benign:1

Apr 18, 2018

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiovascular phenotype Benign:1

Dec 03, 2018

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.46	D
BayesDel_noAF	Pathogenic	0.42
CADD	Pathogenic	33
DANN	Uncertain	1.0
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.95
FATHMM_MKL	Uncertain	0.97	D
PhyloP100		5.9
GERP RS		5.4
Mutation Taster		=78/22	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.79		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.34		Position offset: -4
DS_AL_spliceai		0.79		Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs141281214; hg19: chr12-22015989;