17-34291962-G-A

Position:

• chr17-34291962-G-A

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 0.155 in 152,174 control chromosomes in the GnomAD database, including 2,230 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 (2230 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 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: 0.155 AC: 23561 AN: 152056 Hom.: 2229 Cov.: 31

Gnomad AFR AF: 0.0647

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0884

Gnomad SAS AF: 0.0911

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.155 AC: 23562 AN: 152174 Hom.: 2230 Cov.: 31 AF XY: 0.152 AC XY: 11304 AN XY: 74390

Gnomad4 AFR AF: 0.0646

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.0882

Gnomad4 SAS AF: 0.0912

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.138

Alfa AF: 0.197 Hom.: 1596

Bravo AF: 0.143

Asia WGS AF: 0.0830 AC: 289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4795904; hg19: chr17-32618981;