rs499818

Variant names:

• chr6-13332235-G-A
• rs499818

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 0.215 in 152,190 control chromosomes in the GnomAD database, including 4,015 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 0.21 (4015 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 46 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.405 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: 0.215 AC: 32675 AN: 152072 Hom.: 4009 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.215 AC: 32687 AN: 152190 Hom.: 4015 Cov.: 32 AF XY: 0.215 AC XY: 16023 AN XY: 74396

African (AFR) AF: 0.114 AC: 4747 AN: 41516

American (AMR) AF: 0.295 AC: 4511 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3470

East Asian (EAS) AF: 0.127 AC: 658 AN: 5182

South Asian (SAS) AF: 0.421 AC: 2029 AN: 4824

European-Finnish (FIN) AF: 0.169 AC: 1794 AN: 10588

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17203 AN: 68002

Other (OTH) AF: 0.217 AC: 459 AN: 2114

Alfa AF: 0.242 Hom.: 21987

Bravo AF: 0.215

Asia WGS AF: 0.269 AC: 932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	3.0
DANN	Benign	0.86
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs499818; hg19: chr6-13332467;