17-31656814-G-C

Variant names:

• chr17-31656814-G-C
• rs315437

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;