3-46350297-T-G

Position:

• chr3-46350297-T-G

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 0.132 in 152,270 control chromosomes in the GnomAD database, including 1,569 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 0.13 (1569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20116 AN: 152152 Hom.: 1562 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0633

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0902

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.132 AC: 20151 AN: 152270 Hom.: 1569 Cov.: 32 AF XY: 0.133 AC XY: 9920 AN XY: 74460

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0633

Gnomad4 NFE AF: 0.0902

Gnomad4 OTH AF: 0.137

Alfa AF: 0.0813 Hom.: 138

Bravo AF: 0.145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17141006; hg19: chr3-46391788;