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. The variant received -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
• Publications: 8 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000482980.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCC13	ENST00000482980.5	TSL:1	n.1189+1054G>A		intron	N/A
	ABCC13	ENST00000463099.1	TSL:6	n.1471+575G>A		intron	N/A
	ABCC13	ENST00000688334.2		n.1200+1054G>A		intron	N/A

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

African (AFR) AF: 0.139 AC: 5775 AN: 41492

American (AMR) AF: 0.0898 AC: 1368 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 525 AN: 3468

East Asian (EAS) AF: 0.0429 AC: 222 AN: 5178

South Asian (SAS) AF: 0.0847 AC: 409 AN: 4826

European-Finnish (FIN) AF: 0.0883 AC: 934 AN: 10582

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0637 AC: 4325 AN: 67868

Other (OTH) AF: 0.0906 AC: 191 AN: 2108

Alfa AF: 0.0719 Hom.: 1867

Bravo AF: 0.0937

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0050
DANN	Benign	0.73
PhyloP100		-2.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2192161; hg19: chr21-15681994;