6-32249315-T-C

Variant names:

• chr6-32249315-T-C
• rs6936204

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 0.704 in 151,976 control chromosomes in the GnomAD database, including 38,003 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 0.70 (38003 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 47 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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: 0.703 AC: 106825 AN: 151858 Hom.: 37966 Cov.: 30

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.704 AC: 106919 AN: 151976 Hom.: 38003 Cov.: 30 AF XY: 0.707 AC XY: 52528 AN XY: 74262

African (AFR) AF: 0.717 AC: 29726 AN: 41450

American (AMR) AF: 0.805 AC: 12295 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3126 AN: 3470

East Asian (EAS) AF: 0.827 AC: 4263 AN: 5154

South Asian (SAS) AF: 0.818 AC: 3944 AN: 4824

European-Finnish (FIN) AF: 0.639 AC: 6739 AN: 10548

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44453 AN: 67948

Other (OTH) AF: 0.746 AC: 1573 AN: 2108

Alfa AF: 0.679 Hom.: 111615

Bravo AF: 0.716

Asia WGS AF: 0.824 AC: 2865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.62
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs6936204; hg19: chr6-32217092;