3-39653278-C-T

Variant names:

• chr3-39653278-C-T
• rs1405796

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 0.0972 in 152,004 control chromosomes in the GnomAD database, including 948 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 0.097 (948 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.868

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.138 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: 0.0972 AC: 14765 AN: 151886 Hom.: 945 Cov.: 31

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0625

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0899

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.0940

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

GnomAD4 genome AF: 0.0972 AC: 14774 AN: 152004 Hom.: 948 Cov.: 31 AF XY: 0.0981 AC XY: 7286 AN XY: 74290

Gnomad4 AFR AF: 0.0278

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.0624

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0899

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.0921

Alfa AF: 0.118 Hom.: 1169

Bravo AF: 0.0940

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1405796; hg19: chr3-39694769;