chr10-42965335-T-A

Variant names:

• chr10-42965335-T-A
• rs7908085

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 0.248 in 152,114 control chromosomes in the GnomAD database, including 4,736 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 0.25 (4736 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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: 0.248 AC: 37712 AN: 151996 Hom.: 4725 Cov.: 33

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.248 AC: 37752 AN: 152114 Hom.: 4736 Cov.: 33 AF XY: 0.246 AC XY: 18264 AN XY: 74348

African (AFR) AF: 0.277 AC: 11471 AN: 41468

American (AMR) AF: 0.200 AC: 3063 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 647 AN: 3466

East Asian (EAS) AF: 0.245 AC: 1272 AN: 5188

South Asian (SAS) AF: 0.239 AC: 1156 AN: 4830

European-Finnish (FIN) AF: 0.255 AC: 2703 AN: 10582

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16795 AN: 67976

Other (OTH) AF: 0.237 AC: 501 AN: 2110

Alfa AF: 0.249 Hom.: 609

Bravo AF: 0.245

Asia WGS AF: 0.266 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.85
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs7908085; hg19: chr10-43460783;