3-139887952-G-T

Variant names:

• chr3-139887952-G-T
• rs2554152

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 0.241 in 152,122 control chromosomes in the GnomAD database, including 6,980 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 0.24 (6980 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36594 AN: 152004 Hom.: 6964 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0861

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.241 AC: 36639 AN: 152122 Hom.: 6980 Cov.: 32 AF XY: 0.238 AC XY: 17668 AN XY: 74344

African (AFR) AF: 0.535 AC: 22209 AN: 41474

American (AMR) AF: 0.141 AC: 2157 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3468

East Asian (EAS) AF: 0.221 AC: 1141 AN: 5168

South Asian (SAS) AF: 0.167 AC: 806 AN: 4812

European-Finnish (FIN) AF: 0.0861 AC: 911 AN: 10586

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8267 AN: 68006

Other (OTH) AF: 0.188 AC: 398 AN: 2114

Alfa AF: 0.163 Hom.: 11910

Bravo AF: 0.258

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	15
DANN	Benign	0.88
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs2554152; hg19: chr3-139606794;