3-128532835-C-T

Variant names:

• chr3-128532835-C-T
• rs4431128

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.158 in 151,918 control chromosomes in the GnomAD database, including 2,436 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 0.16 (2436 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24029 AN: 151800 Hom.: 2431 Cov.: 31

Gnomad AFR AF: 0.0495

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.158 AC: 24042 AN: 151918 Hom.: 2436 Cov.: 31 AF XY: 0.164 AC XY: 12137 AN XY: 74202

Gnomad4 AFR AF: 0.0494

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.161

Alfa AF: 0.183 Hom.: 670

Bravo AF: 0.156

Asia WGS AF: 0.243 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4431128; hg19: chr3-128251678;