chr6-33497705-C-T

Variant names:

• chr6-33497705-C-T
• rs9394152

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 0.514 in 152,096 control chromosomes in the GnomAD database, including 22,959 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 0.51 (22959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78152 AN: 151978 Hom.: 22955 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.514 AC: 78172 AN: 152096 Hom.: 22959 Cov.: 32 AF XY: 0.528 AC XY: 39220 AN XY: 74320

African (AFR) AF: 0.228 AC: 9469 AN: 41482

American (AMR) AF: 0.585 AC: 8948 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2017 AN: 3472

East Asian (EAS) AF: 0.879 AC: 4550 AN: 5174

South Asian (SAS) AF: 0.809 AC: 3903 AN: 4822

European-Finnish (FIN) AF: 0.718 AC: 7600 AN: 10580

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.587 AC: 39899 AN: 67968

Other (OTH) AF: 0.518 AC: 1094 AN: 2110

Alfa AF: 0.574 Hom.: 12138

Bravo AF: 0.483

Asia WGS AF: 0.782 AC: 2717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.0
DANN	Benign	0.88
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs9394152; hg19: chr6-33465482;