6-32698749-C-T

Variant names:

• chr6-32698749-C-T
• rs1794282

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 0.0626 in 148,696 control chromosomes in the GnomAD database, including 456 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 0.063 (456 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 48 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0627 AC: 9311 AN: 148586 Hom.: 456 Cov.: 32

Gnomad AFR AF: 0.0151

Gnomad AMI AF: 0.0566

Gnomad AMR AF: 0.0295

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0872

Gnomad MID AF: 0.0192

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0490

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

GnomAD4 genome AF: 0.0626 AC: 9309 AN: 148696 Hom.: 456 Cov.: 32 AF XY: 0.0584 AC XY: 4242 AN XY: 72606

African (AFR) AF: 0.0150 AC: 604 AN: 40232

American (AMR) AF: 0.0294 AC: 442 AN: 15012

Ashkenazi Jewish (ASJ) AF: 0.0392 AC: 133 AN: 3392

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.00 AC: 0 AN: 4730

European-Finnish (FIN) AF: 0.0872 AC: 873 AN: 10006

Middle Eastern (MID) AF: 0.0207 AC: 6 AN: 290

European-Non Finnish (NFE) AF: 0.106 AC: 7103 AN: 66962

Other (OTH) AF: 0.0485 AC: 99 AN: 2042

Alfa AF: 0.0958 Hom.: 2825

Bravo AF: 0.0558

Asia WGS AF: 0.00434 AC: 16 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.7
DANN	Benign	0.65
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1794282; hg19: chr6-32666526;