17-71374289-G-T

Position:

• chr17-71374289-G-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 0.108 in 152,098 control chromosomes in the GnomAD database, including 1,040 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 0.11 (1040 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

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 (EAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16486 AN: 151980 Hom.: 1039 Cov.: 32

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.108 AC: 16491 AN: 152098 Hom.: 1040 Cov.: 32 AF XY: 0.114 AC XY: 8485 AN XY: 74344

Gnomad4 AFR AF: 0.0478

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.113

Alfa AF: 0.114 Hom.: 1868

Bravo AF: 0.102

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.49
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17225585; hg19: chr17-69370430;