rs499384

Positions:

• chr6-33614313-G-A

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 0.115 in 152,156 control chromosomes in the GnomAD database, including 1,052 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 0.12 (1052 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 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: 0.115 AC: 17549 AN: 152038 Hom.: 1051 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.0617

Gnomad FIN AF: 0.0803

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.115 AC: 17556 AN: 152156 Hom.: 1052 Cov.: 32 AF XY: 0.112 AC XY: 8327 AN XY: 74390

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0896

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.0622

Gnomad4 FIN AF: 0.0803

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.123

Alfa AF: 0.107 Hom.: 2025

Bravo AF: 0.121

Asia WGS AF: 0.0990 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.93
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs499384; hg19: chr6-33582090;