5-179108712-A-G

Position:

• chr5-179108712-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 0.711 in 152,124 control chromosomes in the GnomAD database, including 38,653 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 0.71 (38653 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.179108712A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108149 AN: 152006 Hom.: 38630 Cov.: 33

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.711 AC: 108225 AN: 152124 Hom.: 38653 Cov.: 33 AF XY: 0.717 AC XY: 53303 AN XY: 74352

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.742

Alfa AF: 0.687 Hom.: 15694

Bravo AF: 0.714

Asia WGS AF: 0.846 AC: 2940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	3.7
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: rs11750568; hg19: chr5-178535713;