3-117443937-C-T

Variant names:

• chr3-117443937-C-T
• rs4075039

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 0.197 in 152,088 control chromosomes in the GnomAD database, including 3,543 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 0.20 (3543 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 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: 0.197 AC: 29863 AN: 151970 Hom.: 3536 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.197 AC: 29893 AN: 152088 Hom.: 3543 Cov.: 33 AF XY: 0.208 AC XY: 15465 AN XY: 74336

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.209

Alfa AF: 0.181 Hom.: 5545

Bravo AF: 0.193

Asia WGS AF: 0.374 AC: 1296 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.64
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4075039; hg19: chr3-117162784;