10-42939076-C-T

Position:

• chr10-42939076-C-T

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 0.207 in 152,048 control chromosomes in the GnomAD database, including 3,567 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 0.21 (3567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 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: 0.207 AC: 31451 AN: 151930 Hom.: 3567 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0221

Gnomad SAS AF: 0.0874

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.207 AC: 31471 AN: 152048 Hom.: 3567 Cov.: 32 AF XY: 0.201 AC XY: 14923 AN XY: 74326

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0224

Gnomad4 SAS AF: 0.0885

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.170

Alfa AF: 0.206 Hom.: 1079

Bravo AF: 0.204

Asia WGS AF: 0.0750 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs788271; hg19: chr10-43434524;