rs10482853

Positions:

• chr21-14323994-G-C
• chr21-14323994-G-A

Variant summary

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

The ENST00000463099.1(ABCC13):​n.2055+407G>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 0.092 in 150,948 control chromosomes in the GnomAD database, including 728 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 0.092 (728 hom., cov: 28)
• Consequence: ABCC13 ENST00000463099.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.153 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.2055+407G>C		intron_variant, non_coding_transcript_variant
ABCC13	ENST00000482980.5	n.2888+407G>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0922 AC: 13900 AN: 150834 Hom.: 728 Cov.: 28

Gnomad AFR AF: 0.0559

Gnomad AMI AF: 0.0662

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.0920 AC: 13891 AN: 150948 Hom.: 728 Cov.: 28 AF XY: 0.0943 AC XY: 6948 AN XY: 73680

Gnomad4 AFR AF: 0.0557

Gnomad4 AMR AF: 0.0692

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0952

Alfa AF: 0.0889 Hom.: 84

Bravo AF: 0.0869

Asia WGS AF: 0.137 AC: 476 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.92
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10482853; hg19: chr21-15696315;