rs17105882

Variant names:

• chr5-147085799-A-G
• rs17105882

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;