10-62492218-C-T

Position:

• chr10-62492218-C-T

Variant summary

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

The ENST00000647733.1(ENSG00000285837):​c.981+32421C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,972 control chromosomes in the GnomAD database, including 15,153 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 (15153 hom., cov: 31)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183

Genes affected

ENSG00000285837 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.62492218C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285837	ENST00000647733.1	c.981+32421C>T		intron_variant				ENSP00000502188.1

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64860 AN: 151856 Hom.: 15159 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.427 AC: 64860 AN: 151972 Hom.: 15153 Cov.: 31 AF XY: 0.430 AC XY: 31905 AN XY: 74278

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.447

Alfa AF: 0.491 Hom.: 17280

Bravo AF: 0.420

Asia WGS AF: 0.463 AC: 1612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10822013; hg19: chr10-64251977;