chr10-61339792-C-T

Variant names:

• chr10-61339792-C-T
• rs10509145

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 0.378 in 152,034 control chromosomes in the GnomAD database, including 11,878 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 0.38 (11878 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• 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 (NFE) allele frequency at 95% confidence interval = 0.474 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: 0.378 AC: 57428 AN: 151916 Hom.: 11873 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.0938

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.378 AC: 57432 AN: 152034 Hom.: 11878 Cov.: 33 AF XY: 0.371 AC XY: 27594 AN XY: 74322

African (AFR) AF: 0.239 AC: 9885 AN: 41436

American (AMR) AF: 0.339 AC: 5171 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1669 AN: 3472

East Asian (EAS) AF: 0.0936 AC: 484 AN: 5170

South Asian (SAS) AF: 0.314 AC: 1515 AN: 4818

European-Finnish (FIN) AF: 0.452 AC: 4779 AN: 10570

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32505 AN: 67978

Other (OTH) AF: 0.401 AC: 848 AN: 2114

Alfa AF: 0.425 Hom.: 22460

Bravo AF: 0.362

Asia WGS AF: 0.217 AC: 758 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.2
DANN	Benign	0.70
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs10509145; hg19: chr10-63099550;