rs1153315

chr21-14302275-G-C

Variant summary

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

The ENST00000463099.1(ABCC13):n.907+135G>C 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 0.221 in 152,042 control chromosomes in the GnomAD database, including 3,921 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 0.22 (3921 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ABCC13 ENST00000463099.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.811

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 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.907+135G>C		intron_variant, non_coding_transcript_variant
ABCC13	ENST00000482980.5	n.891-3421G>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33574 AN: 151924 Hom.: 3924 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.221 AC: 33579 AN: 152042 Hom.: 3921 Cov.: 33 AF XY: 0.219 AC XY: 16287 AN XY: 74316

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.241

Alfa AF: 0.237 Hom.: 532

Bravo AF: 0.219

Asia WGS AF: 0.0730 AC: 254 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.8
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1153315; hg19: chr21-15674596;