6-67094523-C-T

Position:

• chr6-67094523-C-T

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 0.285 in 151,856 control chromosomes in the GnomAD database, including 6,839 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 0.29 (6839 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.598

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 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: 0.285 AC: 43279 AN: 151738 Hom.: 6829 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.285 AC: 43311 AN: 151856 Hom.: 6839 Cov.: 32 AF XY: 0.293 AC XY: 21739 AN XY: 74184

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.307

Alfa AF: 0.293 Hom.: 8862

Bravo AF: 0.276

Asia WGS AF: 0.529 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9294736; hg19: chr6-67804416;