3-32078407-A-T

Variant names:

• chr3-32078407-A-T
• rs4955135

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 0.708 in 152,216 control chromosomes in the GnomAD database, including 40,632 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 0.71 (40632 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 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: 0.708 AC: 107736 AN: 152098 Hom.: 40619 Cov.: 33

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.708 AC: 107776 AN: 152216 Hom.: 40632 Cov.: 33 AF XY: 0.716 AC XY: 53325 AN XY: 74432

African (AFR) AF: 0.420 AC: 17414 AN: 41508

American (AMR) AF: 0.799 AC: 12215 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2747 AN: 3468

East Asian (EAS) AF: 0.911 AC: 4732 AN: 5194

South Asian (SAS) AF: 0.821 AC: 3962 AN: 4824

European-Finnish (FIN) AF: 0.864 AC: 9156 AN: 10600

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55102 AN: 68014

Other (OTH) AF: 0.703 AC: 1485 AN: 2112

Alfa AF: 0.752 Hom.: 5459

Bravo AF: 0.690

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs4955135; hg19: chr3-32119899;