chr17-47232327-A-G

Position:

• chr17-47232327-A-G

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 0.446 in 152,028 control chromosomes in the GnomAD database, including 16,725 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 0.45 (16725 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.47232327A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67728 AN: 151910 Hom.: 16735 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.446 AC: 67732 AN: 152028 Hom.: 16725 Cov.: 32 AF XY: 0.441 AC XY: 32762 AN XY: 74312

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.490

Alfa AF: 0.539 Hom.: 28044

Bravo AF: 0.427

Asia WGS AF: 0.463 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.089
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11079764; hg19: chr17-45309693;