chr17-71493903-A-G

Position:

• chr17-71493903-A-G

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 0.189 in 152,128 control chromosomes in the GnomAD database, including 2,925 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 0.19 (2925 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) 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: 0.189 AC: 28773 AN: 152010 Hom.: 2926 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0422

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.189 AC: 28782 AN: 152128 Hom.: 2925 Cov.: 31 AF XY: 0.186 AC XY: 13831 AN XY: 74360

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0425

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.217

Alfa AF: 0.218 Hom.: 2144

Bravo AF: 0.180

Asia WGS AF: 0.106 AC: 372 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	3.1
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2190712; hg19: chr17-69490044;