rs2822618

chr21-14353547-G-A

Variant summary

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

The ENST00000463099.1(ABCC13):n.2848-7G>A variant causes a splice region, splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,444 control chromosomes in the GnomAD database, including 24,963 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 0.57 (24905 hom., cov: 32)
  • Exomes 𝑓: 0.52 (58 hom.)
• Consequence: ABCC13 ENST00000463099.1 splice_region, splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 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.2848-7G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86008 AN: 151890 Hom.: 24870 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.582

GnomAD4 exome AF: 0.518 AC: 226 AN: 436 Hom.: 58 Cov.: 0 AF XY: 0.477 AC XY: 126 AN XY: 264

Gnomad4 FIN exome AF: 0.514

Gnomad4 NFE exome AF: 0.667

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.566 AC: 86088 AN: 152008 Hom.: 24905 Cov.: 32 AF XY: 0.563 AC XY: 41795 AN XY: 74296

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.585

Alfa AF: 0.529 Hom.: 43724

Bravo AF: 0.576

Asia WGS AF: 0.608 AC: 2115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.42
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2822618; hg19: chr21-15725868;