10-102851169-G-T

Variant names:

• chr10-102851169-G-T
• rs4290163
• ENST00000440461.3:n.258+3086C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000631443.1(ENSG00000282772):​n.381+339C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,730 control chromosomes in the GnomAD database, including 11,948 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 0.39 (11948 hom., cov: 31)
• Consequence: ENSG00000282772 ENST00000631443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

Genes affected

ENSG00000282772 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 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
ENSG00000282772	ENST00000440461.3	n.258+3086C>A		intron_variant	Intron 1 of 1	5
ENSG00000282772	ENST00000629474.2	n.381+339C>A		intron_variant	Intron 2 of 2	5
ENSG00000282772	ENST00000631443.1	n.381+339C>A		intron_variant	Intron 2 of 2	4
ENSG00000282772	ENST00000632794.1	n.357+339C>A		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59622 AN: 151612 Hom.: 11937 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.393 AC: 59675 AN: 151730 Hom.: 11948 Cov.: 31 AF XY: 0.391 AC XY: 29010 AN XY: 74128

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.401

Alfa AF: 0.396 Hom.: 11762

Bravo AF: 0.393

Asia WGS AF: 0.454 AC: 1574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4290163; hg19: chr10-104610926;