17-40514261-A-G

Variant names:

• chr17-40514261-A-G
• rs17708087

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 0.146 in 151,952 control chromosomes in the GnomAD database, including 2,048 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 (2048 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 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: 0.146 AC: 22124 AN: 151832 Hom.: 2048 Cov.: 30

Gnomad AFR AF: 0.0398

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.146 AC: 22123 AN: 151952 Hom.: 2048 Cov.: 30 AF XY: 0.143 AC XY: 10631 AN XY: 74260

Gnomad4 AFR AF: 0.0397

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.0786

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.143

Alfa AF: 0.188 Hom.: 3063

Bravo AF: 0.135

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17708087; hg19: chr17-38670513;