17-31705401-C-T

Position:

• chr17-31705401-C-T

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 0.173 in 152,136 control chromosomes in the GnomAD database, including 2,774 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 0.17 (2774 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31705401C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26281 AN: 152018 Hom.: 2772 Cov.: 32

Gnomad AFR AF: 0.0462

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.0727

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.173 AC: 26286 AN: 152136 Hom.: 2774 Cov.: 32 AF XY: 0.172 AC XY: 12814 AN XY: 74358

Gnomad4 AFR AF: 0.0461

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.0726

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.178

Alfa AF: 0.231 Hom.: 4651

Bravo AF: 0.163

Asia WGS AF: 0.106 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1551355; hg19: chr17-30032420;