rs292404

Variant names:

• chr5-163673674-A-G
• rs292404

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 0.18 in 152,032 control chromosomes in the GnomAD database, including 2,704 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 0.18 (2704 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 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: 0.180 AC: 27296 AN: 151914 Hom.: 2703 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0259

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.180 AC: 27309 AN: 152032 Hom.: 2704 Cov.: 32 AF XY: 0.179 AC XY: 13296 AN XY: 74314

African (AFR) AF: 0.233 AC: 9648 AN: 41462

American (AMR) AF: 0.187 AC: 2852 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3470

East Asian (EAS) AF: 0.0259 AC: 134 AN: 5166

South Asian (SAS) AF: 0.172 AC: 831 AN: 4828

European-Finnish (FIN) AF: 0.158 AC: 1665 AN: 10546

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11060 AN: 67972

Other (OTH) AF: 0.184 AC: 389 AN: 2112

Alfa AF: 0.170 Hom.: 2969

Bravo AF: 0.185

Asia WGS AF: 0.108 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.1
DANN	Benign	0.58
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs292404; hg19: chr5-163100680;