ENST00000429114.5:n.102-8537C>G

Variant names:

• chr21-14259866-C-G
• rs432114
• ENST00000429114.5:n.102-8537C>G

Variant summary

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

The ENST00000429114.5(ABCC13):​n.102-8537C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,092 control chromosomes in the GnomAD database, including 20,436 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 0.52 (20436 hom., cov: 33)
• Consequence: ABCC13 ENST00000429114.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 2 publications found

Genes affected

ABCC13 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 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	ENST00000429114.5	n.102-8537C>G		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78370 AN: 151974 Hom.: 20426 Cov.: 33

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.516 AC: 78404 AN: 152092 Hom.: 20436 Cov.: 33 AF XY: 0.516 AC XY: 38394 AN XY: 74340

African (AFR) AF: 0.432 AC: 17924 AN: 41470

American (AMR) AF: 0.486 AC: 7427 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2070 AN: 3468

East Asian (EAS) AF: 0.581 AC: 3009 AN: 5176

South Asian (SAS) AF: 0.577 AC: 2786 AN: 4826

European-Finnish (FIN) AF: 0.537 AC: 5672 AN: 10572

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37618 AN: 67980

Other (OTH) AF: 0.543 AC: 1146 AN: 2112

Alfa AF: 0.373 Hom.: 947

Bravo AF: 0.510

Asia WGS AF: 0.599 AC: 2085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.46
DANN	Benign	0.71
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs432114; hg19: chr21-15632187;