chr10-71920635-A-G

Variant names:

• chr10-71920635-A-G
• rs7919639

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 0.239 in 152,138 control chromosomes in the GnomAD database, including 5,272 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 0.24 (5272 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.484
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36334 AN: 152020 Hom.: 5270 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.239 AC: 36350 AN: 152138 Hom.: 5272 Cov.: 32 AF XY: 0.246 AC XY: 18274 AN XY: 74364

African (AFR) AF: 0.140 AC: 5834 AN: 41524

American (AMR) AF: 0.330 AC: 5037 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 602 AN: 3472

East Asian (EAS) AF: 0.681 AC: 3514 AN: 5158

South Asian (SAS) AF: 0.293 AC: 1412 AN: 4826

European-Finnish (FIN) AF: 0.293 AC: 3093 AN: 10572

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16273 AN: 67996

Other (OTH) AF: 0.224 AC: 474 AN: 2114

Alfa AF: 0.239 Hom.: 20388

Bravo AF: 0.241

Asia WGS AF: 0.443 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.0
DANN	Benign	0.26
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs7919639; hg19: chr10-73680393;