rs499384

Variant names:

• chr6-33614313-G-A
• rs499384

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 0.115 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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.154 AC: 6370 AN: 41492

American (AMR) AF: 0.0896 AC: 1370 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 372 AN: 3472

East Asian (EAS) AF: 0.125 AC: 647 AN: 5170

South Asian (SAS) AF: 0.0622 AC: 300 AN: 4826

European-Finnish (FIN) AF: 0.0803 AC: 851 AN: 10592

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7257 AN: 67992

Other (OTH) AF: 0.123 AC: 260 AN: 2114

Alfa AF: 0.109 Hom.: 3408

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
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs499384; hg19: chr6-33582090;