rs830814

Variant names:

• chr5-166379203-A-G
• rs830814

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 0.202 in 152,130 control chromosomes in the GnomAD database, including 3,374 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 0.20 (3374 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 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: 0.202 AC: 30681 AN: 152012 Hom.: 3372 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.202 AC: 30682 AN: 152130 Hom.: 3374 Cov.: 32 AF XY: 0.198 AC XY: 14719 AN XY: 74368

African (AFR) AF: 0.150 AC: 6244 AN: 41520

American (AMR) AF: 0.163 AC: 2499 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3468

East Asian (EAS) AF: 0.213 AC: 1089 AN: 5124

South Asian (SAS) AF: 0.157 AC: 759 AN: 4826

European-Finnish (FIN) AF: 0.180 AC: 1901 AN: 10584

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16919 AN: 67992

Other (OTH) AF: 0.208 AC: 439 AN: 2114

Alfa AF: 0.212 Hom.: 1814

Bravo AF: 0.200

Asia WGS AF: 0.197 AC: 686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.8
DANN	Benign	0.29
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs830814; hg19: chr5-165806208; COSMIC: COSV72967942;