rs3091324

Variant names:

• chr17-34273897-G-T
• rs3091324

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 0.15 in 152,096 control chromosomes in the GnomAD database, including 1,796 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 0.15 (1796 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.176 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: 0.150 AC: 22824 AN: 151978 Hom.: 1796 Cov.: 32

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.150 AC: 22816 AN: 152096 Hom.: 1796 Cov.: 32 AF XY: 0.150 AC XY: 11173 AN XY: 74362

Gnomad4 AFR AF: 0.0906

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.164

Alfa AF: 0.157 Hom.: 372

Bravo AF: 0.146

Asia WGS AF: 0.165 AC: 573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3091324; hg19: chr17-32600916;