10-92409040-G-A

Variant names:

• chr10-92409040-G-A
• rs2263638

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 0.351 in 151,844 control chromosomes in the GnomAD database, including 9,471 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 0.35 (9471 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53157 AN: 151724 Hom.: 9453 Cov.: 30

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.351 AC: 53231 AN: 151844 Hom.: 9471 Cov.: 30 AF XY: 0.347 AC XY: 25715 AN XY: 74210

African (AFR) AF: 0.378 AC: 15663 AN: 41398

American (AMR) AF: 0.359 AC: 5464 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3468

East Asian (EAS) AF: 0.211 AC: 1079 AN: 5124

South Asian (SAS) AF: 0.269 AC: 1293 AN: 4810

European-Finnish (FIN) AF: 0.322 AC: 3398 AN: 10540

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24286 AN: 67956

Other (OTH) AF: 0.347 AC: 731 AN: 2108

Alfa AF: 0.355 Hom.: 26008

Bravo AF: 0.354

Asia WGS AF: 0.252 AC: 880 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	13
DANN	Benign	0.89
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2263638; hg19: chr10-94168797;