10-42939076-C-T

Variant names:

• chr10-42939076-C-T
• rs788271

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;