6-46746068-T-C

Variant names:

• chr6-46746068-T-C
• rs9296510

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 0.2 in 151,746 control chromosomes in the GnomAD database, including 3,449 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 (3449 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30248 AN: 151628 Hom.: 3440 Cov.: 31

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.200 AC: 30278 AN: 151746 Hom.: 3449 Cov.: 31 AF XY: 0.207 AC XY: 15349 AN XY: 74160

African (AFR) AF: 0.121 AC: 5002 AN: 41354

American (AMR) AF: 0.285 AC: 4333 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 980 AN: 3466

East Asian (EAS) AF: 0.165 AC: 848 AN: 5148

South Asian (SAS) AF: 0.475 AC: 2279 AN: 4802

European-Finnish (FIN) AF: 0.229 AC: 2402 AN: 10494

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

European-Non Finnish (NFE) AF: 0.202 AC: 13719 AN: 67942

Other (OTH) AF: 0.219 AC: 462 AN: 2108

Alfa AF: 0.198 Hom.: 6083

Bravo AF: 0.190

Asia WGS AF: 0.332 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.69
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs9296510; hg19: chr6-46713805;