rs2192161

chr21-14309673-G-Achr21-14309673-G-T

Variant summary

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

The ENST00000463099.1(ABCC13):n.1471+575G>A variant causes a intron, non coding transcript 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 ENST00000463099.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80

Genes affected

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCC13	ENST00000463099.1	n.1471+575G>A		intron_variant, non_coding_transcript_variant
ABCC13	ENST00000482980.5	n.1189+1054G>A		intron_variant, non_coding_transcript_variant		1

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;