5-179108712-A-G

Variant names:

• chr5-179108712-A-G
• rs11750568

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 0.711 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.735 AC: 30491 AN: 41498

American (AMR) AF: 0.732 AC: 11190 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2586 AN: 3466

East Asian (EAS) AF: 0.887 AC: 4583 AN: 5168

South Asian (SAS) AF: 0.843 AC: 4070 AN: 4828

European-Finnish (FIN) AF: 0.686 AC: 7257 AN: 10578

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45570 AN: 67980

Other (OTH) AF: 0.742 AC: 1566 AN: 2110

Alfa AF: 0.684 Hom.: 61439

Bravo AF: 0.714

Asia WGS AF: 0.846 AC: 2940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	3.7
DANN	Benign	0.37
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs11750568; hg19: chr5-178535713;