rs9561797

Variant names:

• chr13-95168598-A-G
• rs9561797
• NM_005845.5:c.1824+1934T>C

Your query was ambiguous. Multiple possible variants found:

• chr13-95168598-A-G
• chr13-95168598-A-T

Variant summary

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

The NM_005845.5(ABCC4):​c.1824+1934T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,118 control chromosomes in the GnomAD database, including 8,178 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 0.33 (8178 hom., cov: 32)
• Consequence: ABCC4 NM_005845.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCC4	NM_005845.5	c.1824+1934T>C		intron_variant	Intron 14 of 30	ENST00000645237.2	NP_005836.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCC4	ENST00000645237.2	c.1824+1934T>C		intron_variant	Intron 14 of 30		NM_005845.5	ENSP00000494609.1

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49474 AN: 152000 Hom.: 8165 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.326 AC: 49536 AN: 152118 Hom.: 8178 Cov.: 32 AF XY: 0.330 AC XY: 24536 AN XY: 74344

African (AFR) AF: 0.306 AC: 12689 AN: 41512

American (AMR) AF: 0.307 AC: 4695 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1430 AN: 3468

East Asian (EAS) AF: 0.300 AC: 1551 AN: 5164

South Asian (SAS) AF: 0.360 AC: 1728 AN: 4806

European-Finnish (FIN) AF: 0.395 AC: 4171 AN: 10560

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22013 AN: 67998

Other (OTH) AF: 0.342 AC: 723 AN: 2112

Alfa AF: 0.325 Hom.: 16947

Bravo AF: 0.320

Asia WGS AF: 0.309 AC: 1075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.34
PhyloP100		0.29
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: rs9561797; hg19: chr13-95820852;