3-46486440-T-C

Variant names:

• chr3-46486440-T-C
• rs1402151

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0861 AC: 3574 AN: 41528

American (AMR) AF: 0.344 AC: 5251 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1630 AN: 3468

East Asian (EAS) AF: 0.485 AC: 2501 AN: 5154

South Asian (SAS) AF: 0.399 AC: 1909 AN: 4786

European-Finnish (FIN) AF: 0.430 AC: 4533 AN: 10536

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.397 AC: 26988 AN: 67946

Other (OTH) AF: 0.312 AC: 658 AN: 2106

Alfa AF: 0.367 Hom.: 9154

Bravo AF: 0.300

Asia WGS AF: 0.413 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.46
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1402151; hg19: chr3-46527930;