10-94935594-G-A

Position:

• chr10-94935594-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 0.143 in 152,140 control chromosomes in the GnomAD database, including 1,980 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 0.14 (1980 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21783 AN: 152022 Hom.: 1977 Cov.: 31

Gnomad AFR AF: 0.0523

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.143 AC: 21792 AN: 152140 Hom.: 1980 Cov.: 31 AF XY: 0.148 AC XY: 11033 AN XY: 74388

Gnomad4 AFR AF: 0.0522

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0776 Hom.: 105

Bravo AF: 0.130

Asia WGS AF: 0.294 AC: 1022 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12782374; hg19: chr10-96695351;