rs9349256

chr6-43436773-G-Achr6-43436773-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ABCC10	NM_001198934.2	c.1875+526G>A		intron_variant		ENST00000372530.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCC10	ENST00000372530.9	c.1875+526G>A		intron_variant		2	NM_001198934.2	P2
ABCC10	ENST00000244533.7	c.1791+526G>A		intron_variant		1		A2
ABCC10	ENST00000372515.8	c.543+526G>A		intron_variant		5
ABCC10	ENST00000463024.1	n.220+526G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.384

Alfa AF: 0.443 Hom.: 15318

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

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

Other links and lift over

dbSNP: rs9349256; hg19: chr6-43404511;