chr2-46694146-G-A

Variant names:

• chr2-46694146-G-A
• rs12474201

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 0.298 in 152,104 control chromosomes in the GnomAD database, including 7,289 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 0.30 (7289 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 52 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45280 AN: 151986 Hom.: 7295 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.298 AC: 45291 AN: 152104 Hom.: 7289 Cov.: 32 AF XY: 0.293 AC XY: 21789 AN XY: 74340

African (AFR) AF: 0.205 AC: 8513 AN: 41498

American (AMR) AF: 0.363 AC: 5545 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1250 AN: 3466

East Asian (EAS) AF: 0.143 AC: 741 AN: 5174

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4824

European-Finnish (FIN) AF: 0.275 AC: 2903 AN: 10568

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24220 AN: 67968

Other (OTH) AF: 0.299 AC: 631 AN: 2112

Alfa AF: 0.335 Hom.: 24599

Bravo AF: 0.302

Asia WGS AF: 0.200 AC: 696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs12474201; hg19: chr2-46921285;