6-46746068-T-C

Position:

• chr6-46746068-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;