rs2822557

chr21-14298703-G-A

Variant summary

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

The NR_003087.1(ABCC13):n.891-735G>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 0.114 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 NR_003087.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

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=-0.9).
• 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/exons	MANE	UniProt
ABCC13	NR_003087.1	n.891-735G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCC13	ENST00000463099.1	n.598-735G>A		intron_variant, non_coding_transcript_variant
ABCC13	ENST00000482980.5	n.890+6956G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0292

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.127

Alfa AF: 0.146 Hom.: 3620

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2822557; hg19: chr21-15671024;