chr10-94681893-G-A

Position:

• chr10-94681893-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 0.447 in 152,054 control chromosomes in the GnomAD database, including 16,687 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 0.45 (16687 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.589 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: 0.447 AC: 67901 AN: 151936 Hom.: 16680 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.447 AC: 67915 AN: 152054 Hom.: 16687 Cov.: 32 AF XY: 0.449 AC XY: 33392 AN XY: 74326

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.467

Alfa AF: 0.471 Hom.: 2254

Bravo AF: 0.448

Asia WGS AF: 0.425 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.9
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10736086; hg19: chr10-96441650;