6-67094523-C-T

Variant names:

• chr6-67094523-C-T
• rs9294736

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 0.285 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.169 AC: 6987 AN: 41440

American (AMR) AF: 0.349 AC: 5320 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1038 AN: 3466

East Asian (EAS) AF: 0.568 AC: 2916 AN: 5134

South Asian (SAS) AF: 0.484 AC: 2333 AN: 4816

European-Finnish (FIN) AF: 0.349 AC: 3670 AN: 10506

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.295 AC: 20060 AN: 67944

Other (OTH) AF: 0.307 AC: 648 AN: 2114

Alfa AF: 0.289 Hom.: 10698

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
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs9294736; hg19: chr6-67804416;