chr10-50134990-G-A

Variant names:

• chr10-50134990-G-A
• rs17720367

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 0.179 in 151,250 control chromosomes in the GnomAD database, including 2,750 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 0.18 (2750 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.234 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: 0.179 AC: 27074 AN: 151132 Hom.: 2754 Cov.: 29

Gnomad AFR AF: 0.0763

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0746

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.179 AC: 27067 AN: 151250 Hom.: 2750 Cov.: 29 AF XY: 0.178 AC XY: 13175 AN XY: 73858

African (AFR) AF: 0.0761 AC: 3136 AN: 41192

American (AMR) AF: 0.173 AC: 2619 AN: 15146

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 732 AN: 3454

East Asian (EAS) AF: 0.0744 AC: 386 AN: 5188

South Asian (SAS) AF: 0.171 AC: 812 AN: 4740

European-Finnish (FIN) AF: 0.255 AC: 2658 AN: 10418

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.237 AC: 16082 AN: 67816

Other (OTH) AF: 0.198 AC: 414 AN: 2092

Alfa AF: 0.127 Hom.: 381

Bravo AF: 0.168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.086
DANN	Benign	0.27
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs17720367; hg19: chr10-51894750;