rs2185631

chr6-43440267-A-Gchr6-43440267-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001198934.2(ABCC10):c.2127+1472A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,862 control chromosomes in the GnomAD database, including 14,841 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 0.42 (14841 hom., cov: 31)
• Consequence: ABCC10 NM_001198934.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCC10	NM_001198934.2	c.2127+1472A>G		intron_variant		ENST00000372530.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCC10	ENST00000372530.9	c.2127+1472A>G		intron_variant		2	NM_001198934.2	P2

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63351 AN: 151742 Hom.: 14842 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.417 AC: 63356 AN: 151862 Hom.: 14841 Cov.: 31 AF XY: 0.420 AC XY: 31171 AN XY: 74210

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.411

Alfa AF: 0.485 Hom.: 26958

Bravo AF: 0.396

Asia WGS AF: 0.463 AC: 1609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.8
Dann	Benign	0.61

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: rs2185631; hg19: chr6-43408005;