13-95061461-G-T

Variant names:

• chr13-95061461-G-T
• rs9561778
• NM_005845.5:c.3366+1243C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005845.5(ABCC4):​c.3366+1243C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,958 control chromosomes in the GnomAD database, including 2,485 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 0.17 (2485 hom., cov: 31)
• Consequence: ABCC4 NM_005845.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 25 publications found

Genes affected

ABCC4 (HGNC:55): (ATP binding cassette subfamily C member 4 (PEL blood group)) 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 family member plays a role in cellular detoxification as a pump for its substrate, organic anions. It may also function in prostaglandin-mediated cAMP signaling in ciliogenesis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2014]

ABCC4 Gene-Disease associations (from GenCC):

• qualitative platelet defect

  Inheritance: AR Classification: MODERATE Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005845.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCC4	NM_005845.5	MANE Select	c.3366+1243C>A		intron	N/A	NP_005836.2	O15439-1
	ABCC4	NM_001301829.2		c.3225+1243C>A		intron	N/A	NP_001288758.1	O15439-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCC4	ENST00000645237.2	MANE Select	c.3366+1243C>A		intron	N/A	ENSP00000494609.1	O15439-1
	ABCC4	ENST00000967420.1		c.3366+1243C>A		intron	N/A	ENSP00000637479.1
	ABCC4	ENST00000967421.1		c.3363+1243C>A		intron	N/A	ENSP00000637480.1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26532 AN: 151840 Hom.: 2476 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.143

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.175 AC: 26578 AN: 151958 Hom.: 2485 Cov.: 31 AF XY: 0.171 AC XY: 12706 AN XY: 74254

African (AFR) AF: 0.145 AC: 6016 AN: 41450

American (AMR) AF: 0.121 AC: 1847 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3470

East Asian (EAS) AF: 0.282 AC: 1459 AN: 5182

South Asian (SAS) AF: 0.153 AC: 736 AN: 4810

European-Finnish (FIN) AF: 0.158 AC: 1664 AN: 10534

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13961 AN: 67932

Other (OTH) AF: 0.148 AC: 311 AN: 2106

Alfa AF: 0.180 Hom.: 5241

Bravo AF: 0.171

Asia WGS AF: 0.206 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.074
DANN	Benign	0.68
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9561778; hg19: chr13-95713715;