rs1153315

Variant names:

• chr21-14302275-G-C
• rs1153315
• ENST00000482980.5:n.891-3421G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000482980.5(ABCC13):​n.891-3421G>C variant causes a intron 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 ENST00000482980.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.811
• Publications: 0 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=-0.93).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCC13	ENST00000482980.5	n.891-3421G>C		intron_variant	Intron 5 of 13	1
ABCC13	ENST00000463099.1	n.907+135G>C		intron_variant	Intron 7 of 27	6
ABCC13	ENST00000688334.2	n.902-3421G>C		intron_variant	Intron 5 of 8

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

African (AFR) AF: 0.199 AC: 8272 AN: 41494

American (AMR) AF: 0.209 AC: 3186 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1197 AN: 3466

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5186

South Asian (SAS) AF: 0.123 AC: 594 AN: 4824

European-Finnish (FIN) AF: 0.254 AC: 2682 AN: 10542

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16737 AN: 67944

Other (OTH) AF: 0.241 AC: 509 AN: 2110

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
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs1153315; hg19: chr21-15674596;