rs830814

chr5-166379203-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;