17-31708363-C-T

Variant names:

• chr17-31708363-C-T
• rs315491

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.241 in 151,990 control chromosomes in the GnomAD database, including 5,443 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 0.24 (5443 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 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: 0.241 AC: 36590 AN: 151872 Hom.: 5442 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.241 AC: 36605 AN: 151990 Hom.: 5443 Cov.: 32 AF XY: 0.248 AC XY: 18396 AN XY: 74284

African (AFR) AF: 0.130 AC: 5373 AN: 41436

American (AMR) AF: 0.415 AC: 6335 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3468

East Asian (EAS) AF: 0.597 AC: 3087 AN: 5170

South Asian (SAS) AF: 0.452 AC: 2178 AN: 4818

European-Finnish (FIN) AF: 0.185 AC: 1955 AN: 10570

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16248 AN: 67946

Other (OTH) AF: 0.239 AC: 505 AN: 2110

Alfa AF: 0.237 Hom.: 553

Bravo AF: 0.250

Asia WGS AF: 0.468 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.4
DANN	Benign	0.75
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs315491; hg19: chr17-30035382;