Variant rs8047091 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001370497.1(ABCC11):c.1122A>G(p.Lys374=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,613,234 control chromosomes in the GnomAD database, including 22,434 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.20 ( 3768 hom., cov: 32)

Exomes 𝑓: 0.15 ( 18666 hom. )

Consequence

ABCC11
NM_001370497.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.127

Variant links:

Genes affected

ABCC11 (HGNC:14639): (ATP binding cassette subfamily C member 11) 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 ABC full transporter is a member of the MRP subfamily which is involved in multi-drug resistance. The product of this gene participates in physiological processes involving bile acids, conjugated steroids, and cyclic nucleotides. In addition, a SNP in this gene is responsible for determination of human earwax type. This gene and family member ABCC12 are determined to be derived by duplication and are both localized to chromosome 16q12.1. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Jul 2008]

ABCC11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP7

Synonymous conserved (PhyloP=-0.127 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCC11	NM_001370497.1 linkuse as main transcript	c.1122A>G	p.Lys374=	synonymous_variant	9/30	ENST00000356608.7	NP_001357426.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCC11	ENST00000356608.7 linkuse as main transcript	c.1122A>G	p.Lys374=	synonymous_variant	9/30	1	NM_001370497.1	ENSP00000349017	P1	Q96J66-1

Frequencies

GnomAD3 genomes

AF:

0.203

AC:

30911

AN:

151930

Hom.:

3748

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.134

Gnomad AMR

AF:

0.156

Gnomad ASJ

AF:

0.200

Gnomad EAS

AF:

0.0306

Gnomad SAS

AF:

0.0759

Gnomad FIN

AF:

0.167

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.162

Gnomad OTH

AF:

0.199

GnomAD3 exomes

AF:

0.150

AC:

37508

AN:

250708

Hom.:

3422

AF XY:

0.148

AC XY:

20075

AN XY:

135526

show subpopulations

Gnomad AFR exome

AF:

0.335

Gnomad AMR exome

AF:

0.106

Gnomad ASJ exome

AF:

0.209

Gnomad EAS exome

AF:

0.0295

Gnomad SAS exome

AF:

0.0863

Gnomad FIN exome

AF:

0.167

Gnomad NFE exome

AF:

0.163

Gnomad OTH exome

AF:

0.167

GnomAD4 exome

AF:

0.152

AC:

222653

AN:

1461186

Hom.:

18666

Cov.:

AF XY:

0.151

AC XY:

109952

AN XY:

726908

show subpopulations

Gnomad4 AFR exome

AF:

0.338

Gnomad4 AMR exome

AF:

0.110

Gnomad4 ASJ exome

AF:

0.211

Gnomad4 EAS exome

AF:

0.0139

Gnomad4 SAS exome

AF:

0.0886

Gnomad4 FIN exome

AF:

0.169

Gnomad4 NFE exome

AF:

0.155

Gnomad4 OTH exome

AF:

0.167

GnomAD4 genome

AF:

0.204

AC:

30967

AN:

152048

Hom.:

3768

Cov.:

AF XY:

0.201

AC XY:

14952

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.337

Gnomad4 AMR

AF:

0.156

Gnomad4 ASJ

AF:

0.200

Gnomad4 EAS

AF:

0.0307

Gnomad4 SAS

AF:

0.0748

Gnomad4 FIN

AF:

0.167

Gnomad4 NFE

AF:

0.162

Gnomad4 OTH

AF:

0.198

Alfa

AF:

0.172

Hom.:

5498

Bravo

AF:

0.208

Asia WGS

AF:

0.0840

AC:

293

AN:

3478

EpiCase

AF:

0.172

EpiControl

AF:

0.172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.6

DANN

Benign

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over