ENST00000467409.7:n.424+2007G>T

Variant names:

• chr21-14276164-G-T
• rs2822524
• ENST00000467409.7:n.424+2007G>T

Variant summary

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

The ENST00000467409.7(ABCC13):​n.424+2007G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,866 control chromosomes in the GnomAD database, including 14,784 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 0.43 (14784 hom., cov: 31)
• Consequence: ABCC13 ENST00000467409.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCC13	NR_003087.1	n.359+2007G>T		intron_variant	Intron 1 of 5
ABCC13	NR_003088.1	n.359+2007G>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCC13	ENST00000467409.7	n.424+2007G>T		intron_variant	Intron 1 of 5	1
ABCC13	ENST00000471902.6	n.389+2007G>T		intron_variant	Intron 1 of 4	1
ABCC13	ENST00000481582.5	n.278+2007G>T		intron_variant	Intron 1 of 4	1

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65816 AN: 151748 Hom.: 14776 Cov.: 31

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.434 AC: 65840 AN: 151866 Hom.: 14784 Cov.: 31 AF XY: 0.430 AC XY: 31911 AN XY: 74222

African (AFR) AF: 0.352 AC: 14547 AN: 41354

American (AMR) AF: 0.385 AC: 5874 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2042 AN: 3470

East Asian (EAS) AF: 0.193 AC: 1001 AN: 5174

South Asian (SAS) AF: 0.528 AC: 2536 AN: 4806

European-Finnish (FIN) AF: 0.446 AC: 4704 AN: 10548

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.496 AC: 33722 AN: 67928

Other (OTH) AF: 0.440 AC: 929 AN: 2110

Alfa AF: 0.473 Hom.: 28983

Bravo AF: 0.419

Asia WGS AF: 0.366 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.63
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2822524; hg19: chr21-15648485;