rs2822556

Variant names:

• chr21-14296063-T-C
• rs2822556
• ENST00000467409.7:n.956-3375T>C

Variant summary

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

The ENST00000467409.7(ABCC13):​n.956-3375T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 152,052 control chromosomes in the GnomAD database, including 25,197 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 0.57 (25197 hom., cov: 32)
• Consequence: ABCC13 ENST00000467409.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498
• Publications: 3 publications found

Genes affected

ABCC13 (HGNC:):

ABCC13 (HGNC:16022): (ATP binding cassette subfamily C member 13 (pseudogene)) This gene is a member of the superfamily of genes encoding 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 family member is part of the MRP subfamily, which is involved in multi-drug resistance, but the human locus is now thought to be a pseudogene incapable of encoding a functional ABC protein. Alternative splicing results in multiple transcript variants; however, not all variants have been fully described. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCC13	NR_003087.1	n.891-3375T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCC13	ENST00000467409.7	n.956-3375T>C		intron_variant	Intron 5 of 5	1
ABCC13	ENST00000481582.5	n.3833-3375T>C		intron_variant	Intron 4 of 4	1
ABCC13	ENST00000482980.5	n.890+4316T>C		intron_variant	Intron 5 of 13	1

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86837 AN: 151934 Hom.: 25171 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.572 AC: 86911 AN: 152052 Hom.: 25197 Cov.: 32 AF XY: 0.568 AC XY: 42230 AN XY: 74310

African (AFR) AF: 0.671 AC: 27828 AN: 41460

American (AMR) AF: 0.475 AC: 7251 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1882 AN: 3470

East Asian (EAS) AF: 0.681 AC: 3520 AN: 5170

South Asian (SAS) AF: 0.619 AC: 2983 AN: 4818

European-Finnish (FIN) AF: 0.503 AC: 5316 AN: 10564

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.534 AC: 36320 AN: 67990

Other (OTH) AF: 0.561 AC: 1184 AN: 2112

Alfa AF: 0.555 Hom.: 18171

Bravo AF: 0.571

Asia WGS AF: 0.658 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.46
PhyloP100		0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2822556; hg19: chr21-15668384;