ENST00000463099.1:n.2336+3223G>A

Variant names:

• chr21-14341223-G-A
• rs2178907
• ENST00000463099.1:n.2336+3223G>A

Variant summary

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

The ENST00000463099.1(ABCC13):​n.2336+3223G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,856 control chromosomes in the GnomAD database, including 10,948 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 0.37 (10948 hom., cov: 32)
• Consequence: ABCC13 ENST00000463099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 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	ENST00000463099.1	n.2336+3223G>A		intron_variant	Intron 18 of 27	6

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55734 AN: 151738 Hom.: 10934 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.367 AC: 55782 AN: 151856 Hom.: 10948 Cov.: 32 AF XY: 0.362 AC XY: 26856 AN XY: 74218

African (AFR) AF: 0.498 AC: 20643 AN: 41416

American (AMR) AF: 0.294 AC: 4491 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1388 AN: 3468

East Asian (EAS) AF: 0.509 AC: 2626 AN: 5158

South Asian (SAS) AF: 0.403 AC: 1941 AN: 4822

European-Finnish (FIN) AF: 0.210 AC: 2209 AN: 10536

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21258 AN: 67874

Other (OTH) AF: 0.369 AC: 780 AN: 2114

Alfa AF: 0.336 Hom.: 28576

Bravo AF: 0.379

Asia WGS AF: 0.469 AC: 1630 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.010
DANN	Benign	0.48
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2178907; hg19: chr21-15713544;