rs17720367

Variant names:

• chr10-50134990-G-A
• rs17720367

Your query was ambiguous. Multiple possible variants found:

• chr10-50134990-G-A
• chr10-50134990-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.179 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

Gnomad4 AFR AF: 0.0761

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.0744

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.198

Alfa AF: 0.122 Hom.: 330

Bravo AF: 0.168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17720367; hg19: chr10-51894750;