chr17-31656814-G-C

Position:

• chr17-31656814-G-C

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 0.896 in 152,320 control chromosomes in the GnomAD database, including 61,270 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 0.90 (61270 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.907 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: 0.896 AC: 136430 AN: 152202 Hom.: 61219 Cov.: 34

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.896 AC: 136537 AN: 152320 Hom.: 61270 Cov.: 34 AF XY: 0.899 AC XY: 66982 AN XY: 74490

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.907

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.887

Alfa AF: 0.908 Hom.: 7806

Bravo AF: 0.891

Asia WGS AF: 0.850 AC: 2956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs315437; hg19: chr17-29983833;