17-34247262-A-T

Position:

• chr17-34247262-A-T

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 0.103 in 152,328 control chromosomes in the GnomAD database, including 984 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 0.10 (984 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.951

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 (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15694 AN: 152210 Hom.: 980 Cov.: 33

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.0521

Gnomad EAS AF: 0.000960

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.0662

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0814

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.103 AC: 15706 AN: 152328 Hom.: 984 Cov.: 33 AF XY: 0.101 AC XY: 7543 AN XY: 74500

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0738

Gnomad4 ASJ AF: 0.0521

Gnomad4 EAS AF: 0.000962

Gnomad4 SAS AF: 0.0946

Gnomad4 FIN AF: 0.0662

Gnomad4 NFE AF: 0.0814

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0924 Hom.: 95

Bravo AF: 0.106

Asia WGS AF: 0.0440 AC: 153 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	4.4
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8068314; hg19: chr17-32574281;