3-46486440-T-C

Position:

• chr3-46486440-T-C

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 0.312 in 151,986 control chromosomes in the GnomAD database, including 8,991 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 0.31 (8991 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.497

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 = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47481 AN: 151868 Hom.: 8986 Cov.: 30

Gnomad AFR AF: 0.0862

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.312 AC: 47489 AN: 151986 Hom.: 8991 Cov.: 30 AF XY: 0.316 AC XY: 23472 AN XY: 74258

Gnomad4 AFR AF: 0.0861

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.312

Alfa AF: 0.372 Hom.: 7890

Bravo AF: 0.300

Asia WGS AF: 0.413 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1402151; hg19: chr3-46527930;