10-42934866-T-A

Variant names:

• chr10-42934866-T-A
• rs788273

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 0.302 in 151,892 control chromosomes in the GnomAD database, including 7,221 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 0.30 (7221 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 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: 0.302 AC: 45846 AN: 151776 Hom.: 7213 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.302 AC: 45882 AN: 151892 Hom.: 7221 Cov.: 32 AF XY: 0.296 AC XY: 21941 AN XY: 74238

African (AFR) AF: 0.338 AC: 13995 AN: 41372

American (AMR) AF: 0.241 AC: 3688 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3468

East Asian (EAS) AF: 0.119 AC: 615 AN: 5156

South Asian (SAS) AF: 0.202 AC: 968 AN: 4802

European-Finnish (FIN) AF: 0.299 AC: 3160 AN: 10576

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21846 AN: 67920

Other (OTH) AF: 0.269 AC: 568 AN: 2112

Alfa AF: 0.180 Hom.: 381

Bravo AF: 0.300

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.64
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs788273; hg19: chr10-43430314;