rs2192161

Variant names:

• chr21-14309673-G-A
• rs2192161
• ENST00000482980.5:n.1189+1054G>A

Your query was ambiguous. Multiple possible variants found:

• chr21-14309673-G-A
• chr21-14309673-G-C
• chr21-14309673-G-T

Variant summary

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

The ENST00000482980.5(ABCC13):​n.1189+1054G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0911 in 151,952 control chromosomes in the GnomAD database, including 771 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 0.091 (771 hom., cov: 32)
• Consequence: ABCC13 ENST00000482980.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCC13	ENST00000482980.5	n.1189+1054G>A		intron_variant	Intron 8 of 13	1
ABCC13	ENST00000463099.1	n.1471+575G>A		intron_variant	Intron 12 of 27	6
ABCC13	ENST00000688334.1	n.937+1054G>A		intron_variant	Intron 8 of 8

Frequencies

GnomAD3 genomes AF: 0.0911 AC: 13833 AN: 151834 Hom.: 771 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.0900

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0432

Gnomad SAS AF: 0.0843

Gnomad FIN AF: 0.0883

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0637

Gnomad OTH AF: 0.0906

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

GnomAD4 genome AF: 0.0911 AC: 13841 AN: 151952 Hom.: 771 Cov.: 32 AF XY: 0.0917 AC XY: 6813 AN XY: 74298

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0898

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0429

Gnomad4 SAS AF: 0.0847

Gnomad4 FIN AF: 0.0883

Gnomad4 NFE AF: 0.0637

Gnomad4 OTH AF: 0.0906

Alfa AF: 0.0695 Hom.: 845

Bravo AF: 0.0937

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0050
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2192161; hg19: chr21-15681994;