rs4920832

Variant names:

• chr5-85747626-G-A
• rs4920832

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 0.827 in 151,878 control chromosomes in the GnomAD database, including 52,186 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 0.83 (52186 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125510 AN: 151760 Hom.: 52138 Cov.: 31

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.827 AC: 125614 AN: 151878 Hom.: 52186 Cov.: 31 AF XY: 0.823 AC XY: 61056 AN XY: 74230

African (AFR) AF: 0.851 AC: 35319 AN: 41490

American (AMR) AF: 0.759 AC: 11573 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.862 AC: 2994 AN: 3472

East Asian (EAS) AF: 0.580 AC: 2973 AN: 5124

South Asian (SAS) AF: 0.813 AC: 3919 AN: 4818

European-Finnish (FIN) AF: 0.832 AC: 8768 AN: 10544

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57296 AN: 67872

Other (OTH) AF: 0.809 AC: 1709 AN: 2112

Alfa AF: 0.835 Hom.: 42467

Bravo AF: 0.824

Asia WGS AF: 0.723 AC: 2498 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.054
DANN	Benign	0.36
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs4920832; hg19: chr5-85043444;