10-52777079-T-G

Variant names:

• chr10-52777079-T-G
• rs7899547

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 0.707 in 151,844 control chromosomes in the GnomAD database, including 38,307 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 0.71 (38307 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 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: 0.706 AC: 107189 AN: 151726 Hom.: 38256 Cov.: 31

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.707 AC: 107301 AN: 151844 Hom.: 38307 Cov.: 31 AF XY: 0.706 AC XY: 52368 AN XY: 74208

African (AFR) AF: 0.830 AC: 34393 AN: 41424

American (AMR) AF: 0.705 AC: 10758 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2387 AN: 3472

East Asian (EAS) AF: 0.660 AC: 3398 AN: 5148

South Asian (SAS) AF: 0.638 AC: 3069 AN: 4810

European-Finnish (FIN) AF: 0.652 AC: 6852 AN: 10508

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44085 AN: 67900

Other (OTH) AF: 0.694 AC: 1462 AN: 2106

Alfa AF: 0.669 Hom.: 39179

Bravo AF: 0.719

Asia WGS AF: 0.677 AC: 2354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs7899547; hg19: chr10-54536839;