rs17105882

chr5-147085799-A-G

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 0.0969 in 152,142 control chromosomes in the GnomAD database, including 767 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 0.097 (767 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.693

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0968 AC: 14715 AN: 152022 Hom.: 765 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.0572

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0943

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.0957

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

GnomAD4 genome AF: 0.0969 AC: 14736 AN: 152142 Hom.: 767 Cov.: 32 AF XY: 0.0990 AC XY: 7364 AN XY: 74372

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.0571

Gnomad4 ASJ AF: 0.0752

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.0941

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0745

Gnomad4 OTH AF: 0.0942

Alfa AF: 0.0811 Hom.: 172

Bravo AF: 0.0950

Asia WGS AF: 0.147 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.050
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17105882; hg19: chr5-146465362;