17-37746322-G-T

Position:

• chr17-37746322-G-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 0.682 in 152,212 control chromosomes in the GnomAD database, including 36,504 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 0.68 (36504 hom., cov: 35)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37746322G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103797 AN: 152094 Hom.: 36487 Cov.: 35

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.682 AC: 103847 AN: 152212 Hom.: 36504 Cov.: 35 AF XY: 0.670 AC XY: 49842 AN XY: 74424

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.695

Alfa AF: 0.659 Hom.: 27177

Bravo AF: 0.690

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.8

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3760511; hg19: chr17-36106313;