rs2822557

Variant names:

• chr21-14298703-G-A
• rs2822557
• ENST00000467409.7:n.956-735G>A

Variant summary

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

The ENST00000467409.7(ABCC13):​n.956-735G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 151,732 control chromosomes in the GnomAD database, including 1,263 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 0.11 (1263 hom., cov: 31)
• Consequence: ABCC13 ENST00000467409.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCC13	NR_003087.1	n.891-735G>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCC13	ENST00000467409.7	n.956-735G>A		intron_variant	Intron 5 of 5	1
ABCC13	ENST00000481582.5	n.3833-735G>A		intron_variant	Intron 4 of 4	1
ABCC13	ENST00000482980.5	n.890+6956G>A		intron_variant	Intron 5 of 13	1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17236 AN: 151616 Hom.: 1263 Cov.: 31

Gnomad AFR AF: 0.0294

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.138

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.114 AC: 17225 AN: 151732 Hom.: 1263 Cov.: 31 AF XY: 0.114 AC XY: 8432 AN XY: 74160

African (AFR) AF: 0.0292 AC: 1212 AN: 41442

American (AMR) AF: 0.106 AC: 1617 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 630 AN: 3468

East Asian (EAS) AF: 0.163 AC: 841 AN: 5158

South Asian (SAS) AF: 0.139 AC: 670 AN: 4804

European-Finnish (FIN) AF: 0.143 AC: 1493 AN: 10426

Middle Eastern (MID) AF: 0.141 AC: 41 AN: 290

European-Non Finnish (NFE) AF: 0.152 AC: 10300 AN: 67902

Other (OTH) AF: 0.127 AC: 268 AN: 2106

Alfa AF: 0.139 Hom.: 5125

Bravo AF: 0.109

Asia WGS AF: 0.138 AC: 480 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.19
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2822557; hg19: chr21-15671024;