rs3091316

Variant names:

• chr17-34266955-G-A
• rs3091316

Your query was ambiguous. Multiple possible variants found:

• chr17-34266955-G-A
• chr17-34266955-G-C

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 0.289 in 152,046 control chromosomes in the GnomAD database, including 6,979 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 0.29 (6979 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 38 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 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: 0.289 AC: 43841 AN: 151928 Hom.: 6966 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.289 AC: 43882 AN: 152046 Hom.: 6979 Cov.: 32 AF XY: 0.298 AC XY: 22118 AN XY: 74324

African (AFR) AF: 0.207 AC: 8582 AN: 41462

American (AMR) AF: 0.432 AC: 6603 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3470

East Asian (EAS) AF: 0.556 AC: 2880 AN: 5180

South Asian (SAS) AF: 0.344 AC: 1660 AN: 4822

European-Finnish (FIN) AF: 0.345 AC: 3645 AN: 10556

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18708 AN: 67972

Other (OTH) AF: 0.287 AC: 604 AN: 2108

Alfa AF: 0.275 Hom.: 13876

Bravo AF: 0.292

Asia WGS AF: 0.441 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.66
DANN	Benign	0.51
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs3091316; hg19: chr17-32593974;