6-32576834-T-C

Variant names:

• chr6-32576834-T-C
• rs35079132

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.0029 (1 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 10 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

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: 0.00288 AC: 334 AN: 115918 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.00193

Gnomad AMI AF: 0.00372

Gnomad AMR AF: 0.00473

Gnomad ASJ AF: 0.00525

Gnomad EAS AF: 0.00291

Gnomad SAS AF: 0.00333

Gnomad FIN AF: 0.00337

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00293

Gnomad OTH AF: 0.00249

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00287 AC: 333 AN: 116018 Hom.: 1 Cov.: 31 AF XY: 0.00290 AC XY: 164 AN XY: 56602

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00196 AC: 68 AN: 34744

American (AMR) AF: 0.00453 AC: 48 AN: 10588

Ashkenazi Jewish (ASJ) AF: 0.00525 AC: 13 AN: 2476

East Asian (EAS) AF: 0.00293 AC: 10 AN: 3418

South Asian (SAS) AF: 0.00305 AC: 11 AN: 3602

European-Finnish (FIN) AF: 0.00337 AC: 27 AN: 8022

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 224

European-Non Finnish (NFE) AF: 0.00295 AC: 150 AN: 50778

Other (OTH) AF: 0.00246 AC: 4 AN: 1628

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0203 Hom.: 36

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.29
DANN	Benign	0.47
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs35079132; hg19: chr6-32544611; COSMIC: COSV63511499;