3-152834401-C-T

Variant names:

• chr3-152834401-C-T
• rs1371097

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 0.31 in 151,810 control chromosomes in the GnomAD database, including 11,328 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 0.31 (11328 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 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: 0.310 AC: 46998 AN: 151692 Hom.: 11289 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.310 AC: 47092 AN: 151810 Hom.: 11328 Cov.: 32 AF XY: 0.308 AC XY: 22823 AN XY: 74146

African (AFR) AF: 0.676 AC: 27991 AN: 41392

American (AMR) AF: 0.241 AC: 3678 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3466

East Asian (EAS) AF: 0.270 AC: 1393 AN: 5158

South Asian (SAS) AF: 0.216 AC: 1037 AN: 4806

European-Finnish (FIN) AF: 0.143 AC: 1501 AN: 10466

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10109 AN: 67950

Other (OTH) AF: 0.284 AC: 599 AN: 2106

Alfa AF: 0.217 Hom.: 7664

Bravo AF: 0.337

Asia WGS AF: 0.273 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.42
DANN	Benign	0.74
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1371097; hg19: chr3-152552190;