3-106345116-C-T

Variant names:

• chr3-106345116-C-T
• rs6437662

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 0.939 in 152,210 control chromosomes in the GnomAD database, including 67,076 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 0.94 (67076 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 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: 0.939 AC: 142776 AN: 152092 Hom.: 67023 Cov.: 30

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.939 AC: 142888 AN: 152210 Hom.: 67076 Cov.: 30 AF XY: 0.937 AC XY: 69751 AN XY: 74412

African (AFR) AF: 0.943 AC: 39163 AN: 41534

American (AMR) AF: 0.959 AC: 14656 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3246 AN: 3472

East Asian (EAS) AF: 0.965 AC: 4991 AN: 5172

South Asian (SAS) AF: 0.872 AC: 4205 AN: 4824

European-Finnish (FIN) AF: 0.930 AC: 9843 AN: 10580

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.936 AC: 63692 AN: 68022

Other (OTH) AF: 0.943 AC: 1994 AN: 2114

Alfa AF: 0.936 Hom.: 118486

Bravo AF: 0.943

Asia WGS AF: 0.943 AC: 3276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.66
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6437662; hg19: chr3-106063963;