10-42939076-C-T

Variant names:

• chr10-42939076-C-T
• rs788271

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.261 AC: 10801 AN: 41438

American (AMR) AF: 0.124 AC: 1901 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3472

East Asian (EAS) AF: 0.0224 AC: 116 AN: 5182

South Asian (SAS) AF: 0.0885 AC: 426 AN: 4812

European-Finnish (FIN) AF: 0.218 AC: 2301 AN: 10564

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14810 AN: 67984

Other (OTH) AF: 0.170 AC: 359 AN: 2110

Alfa AF: 0.209 Hom.: 1395

Bravo AF: 0.204

Asia WGS AF: 0.0750 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.22
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs788271; hg19: chr10-43434524;