NM_001198934.2:c.2913T>C

Variant names:

• chr6-43445197-T-C
• rs2125740
• NM_001198934.2:c.2913T>C

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001198934.2(ABCC10):​c.2913T>C​(p.Tyr971Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0105 in 1,614,042 control chromosomes in the GnomAD database, including 1,464 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 0.056 (757 hom., cov: 32)
  • Exomes 𝑓: 0.0058 (707 hom.)
• Consequence: ABCC10 NM_001198934.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419
• Publications: 7 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BP7: Synonymous conserved (PhyloP=-0.419 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001198934.2. 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
	ABCC10	NM_001198934.2	MANE Select	c.2913T>C	p.Tyr971Tyr	synonymous	Exon 14 of 22	NP_001185863.1
	ABCC10	NM_033450.3		c.2829T>C	p.Tyr943Tyr	synonymous	Exon 12 of 20	NP_258261.2
	ABCC10	NM_001350518.2		c.1581T>C	p.Tyr527Tyr	synonymous	Exon 14 of 22	NP_001337447.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCC10	ENST00000372530.9	TSL:2 MANE Select	c.2913T>C	p.Tyr971Tyr	synonymous	Exon 14 of 22	ENSP00000361608.4
	ABCC10	ENST00000244533.7	TSL:1	c.2829T>C	p.Tyr943Tyr	synonymous	Exon 12 of 20	ENSP00000244533.3
	ABCC10	ENST00000921385.1		c.2958T>C	p.Tyr986Tyr	synonymous	Exon 14 of 22	ENSP00000591444.1

Frequencies

GnomAD3 genomes AF: 0.0555 AC: 8435 AN: 152072 Hom.: 756 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0176

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.000824

Gnomad OTH AF: 0.0512

GnomAD2 exomes AF: 0.0145 AC: 3650 AN: 251458 AF XY: 0.0105

Gnomad AFR exome AF: 0.196

Gnomad AMR exome AF: 0.00957

Gnomad ASJ exome AF: 0.0000992

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000462

Gnomad NFE exome AF: 0.000598

Gnomad OTH exome AF: 0.00831

GnomAD4 exome AF: 0.00583 AC: 8528 AN: 1461852 Hom.: 707 Cov.: 35 AF XY: 0.00495 AC XY: 3599 AN XY: 727238

African (AFR) AF: 0.201 AC: 6738 AN: 33478

American (AMR) AF: 0.0110 AC: 494 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.000153 AC: 4 AN: 26132

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.000383 AC: 33 AN: 86258

European-Finnish (FIN) AF: 0.0000187 AC: 1 AN: 53420

Middle Eastern (MID) AF: 0.0151 AC: 87 AN: 5766

European-Non Finnish (NFE) AF: 0.000353 AC: 393 AN: 1111984

Other (OTH) AF: 0.0129 AC: 778 AN: 60392

GnomAD4 genome AF: 0.0556 AC: 8457 AN: 152190 Hom.: 757 Cov.: 32 AF XY: 0.0531 AC XY: 3951 AN XY: 74414

African (AFR) AF: 0.193 AC: 8016 AN: 41486

American (AMR) AF: 0.0175 AC: 268 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10614

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.000824 AC: 56 AN: 67990

Other (OTH) AF: 0.0507 AC: 107 AN: 2110

Alfa AF: 0.0180 Hom.: 657

Bravo AF: 0.0638

Asia WGS AF: 0.0100 AC: 36 AN: 3462

EpiCase AF: 0.000491

EpiControl AF: 0.000948

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	0.29
DANN	Benign	0.35
PhyloP100		-0.42
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs2125740; hg19: chr6-43412935;