rs699946

Variant names:

• chr6-43764932-A-G
• rs699946

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 0.204 in 151,852 control chromosomes in the GnomAD database, including 3,329 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 (3329 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520
• Publications: 54 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30930 AN: 151732 Hom.: 3324 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.204 AC: 30946 AN: 151852 Hom.: 3329 Cov.: 31 AF XY: 0.205 AC XY: 15206 AN XY: 74216

African (AFR) AF: 0.186 AC: 7690 AN: 41392

American (AMR) AF: 0.251 AC: 3824 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 932 AN: 3470

East Asian (EAS) AF: 0.411 AC: 2113 AN: 5142

South Asian (SAS) AF: 0.231 AC: 1108 AN: 4798

European-Finnish (FIN) AF: 0.180 AC: 1897 AN: 10546

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12740 AN: 67926

Other (OTH) AF: 0.218 AC: 460 AN: 2108

Alfa AF: 0.202 Hom.: 12739

Bravo AF: 0.214

Asia WGS AF: 0.277 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.25
DANN	Benign	0.33
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs699946; hg19: chr6-43732669;