3-12447383-G-C

Variant names:

• chr3-12447383-G-C
• rs4684854

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 0.352 in 152,126 control chromosomes in the GnomAD database, including 11,977 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 0.35 (11977 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 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: 0.352 AC: 53536 AN: 152008 Hom.: 11980 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.352 AC: 53540 AN: 152126 Hom.: 11977 Cov.: 32 AF XY: 0.361 AC XY: 26821 AN XY: 74382

African (AFR) AF: 0.106 AC: 4395 AN: 41514

American (AMR) AF: 0.374 AC: 5715 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1123 AN: 3468

East Asian (EAS) AF: 0.913 AC: 4735 AN: 5186

South Asian (SAS) AF: 0.618 AC: 2980 AN: 4824

European-Finnish (FIN) AF: 0.471 AC: 4972 AN: 10556

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28548 AN: 67966

Other (OTH) AF: 0.349 AC: 736 AN: 2110

Alfa AF: 0.241 Hom.: 668

Bravo AF: 0.333

Asia WGS AF: 0.624 AC: 2170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.38
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs4684854; hg19: chr3-12488882;