rs9349256

Variant names:

• chr6-43436773-G-A
• rs9349256
• NM_001198934.2:c.1875+526G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-43436773-G-A
• chr6-43436773-G-T

Variant summary

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

The NM_001198934.2(ABCC10):​c.1875+526G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,062 control chromosomes in the GnomAD database, including 13,401 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 0.38 (13401 hom., cov: 32)
• Consequence: ABCC10 NM_001198934.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260
• Publications: 22 publications found

Genes affected

ABCC10 (HGNC:52): (ATP binding cassette subfamily C member 10) 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, and White). This ABC full-transporter is a member of the MRP subfamily which is involved in multi-drug resistance. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Nov 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCC10	NM_001198934.2	c.1875+526G>A		intron_variant	Intron 6 of 21	ENST00000372530.9	NP_001185863.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCC10	ENST00000372530.9	c.1875+526G>A		intron_variant	Intron 6 of 21	2	NM_001198934.2	ENSP00000361608.4
ABCC10	ENST00000244533.7	c.1791+526G>A		intron_variant	Intron 4 of 19	1		ENSP00000244533.3
ABCC10	ENST00000372515.9	c.543+526G>A		intron_variant	Intron 5 of 7	5		ENSP00000361593.4
ABCC10	ENST00000463024.1	n.220+526G>A		intron_variant	Intron 2 of 15	2

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57615 AN: 151944 Hom.: 13408 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.379 AC: 57608 AN: 152062 Hom.: 13401 Cov.: 32 AF XY: 0.384 AC XY: 28558 AN XY: 74332

African (AFR) AF: 0.101 AC: 4197 AN: 41530

American (AMR) AF: 0.401 AC: 6122 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1558 AN: 3470

East Asian (EAS) AF: 0.630 AC: 3252 AN: 5164

South Asian (SAS) AF: 0.442 AC: 2128 AN: 4818

European-Finnish (FIN) AF: 0.559 AC: 5893 AN: 10550

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32923 AN: 67954

Other (OTH) AF: 0.384 AC: 811 AN: 2114

Alfa AF: 0.440 Hom.: 42306

Bravo AF: 0.356

Asia WGS AF: 0.494 AC: 1719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	8.0
DANN	Benign	0.92
PhyloP100		-0.26
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: rs9349256; hg19: chr6-43404511;