10-35771381-A-G

Variant names:

• chr10-35771381-A-G
• rs11010290

Variant summary

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

The variant allele was found at a frequency of 0.122 in 152,084 control chromosomes in the GnomAD database, including 1,476 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 0.12 (1476 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18632 AN: 151966 Hom.: 1477 Cov.: 32

Gnomad AFR AF: 0.0394

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.0924

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0545

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.0906

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

GnomAD4 genome AF: 0.122 AC: 18630 AN: 152084 Hom.: 1476 Cov.: 32 AF XY: 0.127 AC XY: 9455 AN XY: 74354

African (AFR) AF: 0.0393 AC: 1632 AN: 41512

American (AMR) AF: 0.0922 AC: 1409 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3470

East Asian (EAS) AF: 0.0543 AC: 281 AN: 5178

South Asian (SAS) AF: 0.228 AC: 1097 AN: 4810

European-Finnish (FIN) AF: 0.220 AC: 2321 AN: 10548

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11126 AN: 67976

Other (OTH) AF: 0.0925 AC: 195 AN: 2108

Alfa AF: 0.139 Hom.: 3411

Bravo AF: 0.105

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.8
DANN	Benign	0.56
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs11010290; hg19: chr10-36060309;