chr10-92409040-G-A

Position:

• chr10-92409040-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.347

Alfa AF: 0.357 Hom.: 8913

Bravo AF: 0.354

Asia WGS AF: 0.252 AC: 880 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2263638; hg19: chr10-94168797;