6-46746068-T-C

Variant names:

• chr6-46746068-T-C
• rs9296510

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.199 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

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.219

Alfa AF: 0.204 Hom.: 1915

Bravo AF: 0.190

Asia WGS AF: 0.332 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9296510; hg19: chr6-46713805;