rs3091324

Variant names:

• chr17-34273897-G-T
• rs3091324

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 0.15 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0906 AC: 3760 AN: 41496

American (AMR) AF: 0.145 AC: 2220 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 770 AN: 3472

East Asian (EAS) AF: 0.178 AC: 918 AN: 5158

South Asian (SAS) AF: 0.156 AC: 750 AN: 4816

European-Finnish (FIN) AF: 0.166 AC: 1754 AN: 10574

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12158 AN: 67978

Other (OTH) AF: 0.164 AC: 347 AN: 2112

Alfa AF: 0.160 Hom.: 706

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
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs3091324; hg19: chr17-32600916;