ENST00000482980.5:n.2888+407G>C

Variant names:

• chr21-14323994-G-C
• rs10482853
• ENST00000482980.5:n.2888+407G>C

Variant summary

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

The ENST00000482980.5(ABCC13):​n.2888+407G>C variant causes a intron 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 ENST00000482980.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 3 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=-0.91).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCC13	ENST00000482980.5	n.2888+407G>C		intron_variant	Intron 11 of 13	1
ABCC13	ENST00000463099.1	n.2055+407G>C		intron_variant	Intron 16 of 27	6
ABCC13	ENST00000826966.1	n.76+407G>C		intron_variant	Intron 1 of 2
ENSG00000307579	ENST00000827203.1	n.182+3228C>G		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.0557 AC: 2288 AN: 41090

American (AMR) AF: 0.0692 AC: 1047 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 512 AN: 3460

East Asian (EAS) AF: 0.162 AC: 830 AN: 5122

South Asian (SAS) AF: 0.131 AC: 625 AN: 4760

European-Finnish (FIN) AF: 0.136 AC: 1400 AN: 10294

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.102 AC: 6903 AN: 67814

Other (OTH) AF: 0.0952 AC: 199 AN: 2090

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10482853; hg19: chr21-15696315;