chr6-46738856-G-A

Variant names:

• chr6-46738856-G-A
• rs9349373

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 0.206 in 152,020 control chromosomes in the GnomAD database, including 3,583 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 (3583 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.46 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: 0.206 AC: 31247 AN: 151902 Hom.: 3574 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.206 AC: 31279 AN: 152020 Hom.: 3583 Cov.: 32 AF XY: 0.213 AC XY: 15847 AN XY: 74314

African (AFR) AF: 0.142 AC: 5899 AN: 41466

American (AMR) AF: 0.287 AC: 4381 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 983 AN: 3470

East Asian (EAS) AF: 0.165 AC: 851 AN: 5164

South Asian (SAS) AF: 0.476 AC: 2286 AN: 4802

European-Finnish (FIN) AF: 0.228 AC: 2404 AN: 10556

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.202 AC: 13754 AN: 67962

Other (OTH) AF: 0.221 AC: 468 AN: 2116

Alfa AF: 0.205 Hom.: 434

Bravo AF: 0.198

Asia WGS AF: 0.336 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.56
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs9349373; hg19: chr6-46706593;