3-3232153-C-T

Variant names:

• chr3-3232153-C-T
• rs4055307

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 0.568 in 151,856 control chromosomes in the GnomAD database, including 24,803 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 0.57 (24803 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 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: 0.568 AC: 86200 AN: 151740 Hom.: 24780 Cov.: 31

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.568 AC: 86262 AN: 151856 Hom.: 24803 Cov.: 31 AF XY: 0.563 AC XY: 41762 AN XY: 74190

African (AFR) AF: 0.620 AC: 25678 AN: 41416

American (AMR) AF: 0.483 AC: 7367 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2371 AN: 3468

East Asian (EAS) AF: 0.380 AC: 1952 AN: 5134

South Asian (SAS) AF: 0.538 AC: 2586 AN: 4806

European-Finnish (FIN) AF: 0.555 AC: 5854 AN: 10540

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38445 AN: 67924

Other (OTH) AF: 0.562 AC: 1189 AN: 2114

Alfa AF: 0.567 Hom.: 13745

Bravo AF: 0.564

Asia WGS AF: 0.458 AC: 1591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.38
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs4055307; hg19: chr3-3273837;