chr6-33097957-C-A

Variant names:

• chr6-33097957-C-A
• rs2179915

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 0.132 in 151,810 control chromosomes in the GnomAD database, including 2,544 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 0.13 (2544 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 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: 0.132 AC: 20039 AN: 151694 Hom.: 2539 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0687

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.0667

Gnomad FIN AF: 0.0510

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0563

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.132 AC: 20062 AN: 151810 Hom.: 2544 Cov.: 31 AF XY: 0.128 AC XY: 9489 AN XY: 74200

African (AFR) AF: 0.337 AC: 13932 AN: 41354

American (AMR) AF: 0.0686 AC: 1047 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3468

East Asian (EAS) AF: 0.0127 AC: 66 AN: 5182

South Asian (SAS) AF: 0.0664 AC: 320 AN: 4822

European-Finnish (FIN) AF: 0.0510 AC: 533 AN: 10456

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0563 AC: 3828 AN: 67948

Other (OTH) AF: 0.118 AC: 250 AN: 2114

Alfa AF: 0.0771 Hom.: 712

Bravo AF: 0.141

Asia WGS AF: 0.0880 AC: 307 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.14
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2179915; hg19: chr6-33065734;