3-46352479-C-A

Position:

• chr3-46352479-C-A

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 152,090 control chromosomes in the GnomAD database, including 1,568 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 (1568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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: 20098 AN: 151972 Hom.: 1561 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0634

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0901

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: 20133 AN: 152090 Hom.: 1568 Cov.: 32 AF XY: 0.133 AC XY: 9913 AN XY: 74372

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0634

Gnomad4 NFE AF: 0.0901

Gnomad4 OTH AF: 0.137

Alfa AF: 0.0553 Hom.: 61

Bravo AF: 0.145

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3918357; hg19: chr3-46393970;