ENST00000787871.1:n.427-3801G>A

Variant names:

• chr13-103528870-G-A
• rs10508112
• ENST00000787871.1:n.427-3801G>A

Variant summary

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

The ENST00000787871.1(ENSG00000302562):​n.427-3801G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0532 in 151,988 control chromosomes in the GnomAD database, including 342 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 0.053 (342 hom., cov: 32)
• Consequence: ENSG00000302562 ENST00000787871.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 0 publications found

Genes affected

ENSG00000302562 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 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
ENSG00000302562	ENST00000787871.1	n.427-3801G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0531 AC: 8063 AN: 151870 Hom.: 342 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0379

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.00716

Gnomad SAS AF: 0.0278

Gnomad FIN AF: 0.0220

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0349

Gnomad OTH AF: 0.0489

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

GnomAD4 genome AF: 0.0532 AC: 8079 AN: 151988 Hom.: 342 Cov.: 32 AF XY: 0.0517 AC XY: 3844 AN XY: 74284

African (AFR) AF: 0.108 AC: 4495 AN: 41486

American (AMR) AF: 0.0378 AC: 576 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3464

East Asian (EAS) AF: 0.00698 AC: 36 AN: 5156

South Asian (SAS) AF: 0.0276 AC: 133 AN: 4818

European-Finnish (FIN) AF: 0.0220 AC: 233 AN: 10584

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0349 AC: 2373 AN: 67936

Other (OTH) AF: 0.0521 AC: 110 AN: 2110

Alfa AF: 0.0507 Hom.: 41

Bravo AF: 0.0568

Asia WGS AF: 0.0380 AC: 132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.41
DANN	Benign	0.60
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs10508112; hg19: chr13-104181220;