rs830814

Variant names:

• chr5-166379203-A-G
• rs830814

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 0.202 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.208

Alfa AF: 0.223 Hom.: 734

Bravo AF: 0.200

Asia WGS AF: 0.197 AC: 686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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