10-62492218-C-T

Variant names:

• chr10-62492218-C-T
• rs10822013
• ENST00000647733.1:c.981+32421C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 58 publications found

Genes affected

ENSG00000285837 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647733.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285837	ENST00000647733.1		c.981+32421C>T		intron	N/A	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

African (AFR) AF: 0.230 AC: 9523 AN: 41466

American (AMR) AF: 0.491 AC: 7498 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1619 AN: 3462

East Asian (EAS) AF: 0.489 AC: 2526 AN: 5166

South Asian (SAS) AF: 0.492 AC: 2372 AN: 4820

European-Finnish (FIN) AF: 0.468 AC: 4938 AN: 10554

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34944 AN: 67942

Other (OTH) AF: 0.447 AC: 940 AN: 2104

Alfa AF: 0.483 Hom.: 56083

Bravo AF: 0.420

Asia WGS AF: 0.463 AC: 1612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.65
PhyloP100		0.18
Mutation Taster		=99/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10822013; hg19: chr10-64251977;