2-433274-A-G

Variant names:

• chr2-433274-A-G
• rs4854306

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 0.234 in 152,114 control chromosomes in the GnomAD database, including 4,321 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 0.23 (4321 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.940
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.283 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: 0.234 AC: 35503 AN: 151996 Hom.: 4316 Cov.: 33

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.234 AC: 35536 AN: 152114 Hom.: 4321 Cov.: 33 AF XY: 0.234 AC XY: 17371 AN XY: 74366

African (AFR) AF: 0.251 AC: 10404 AN: 41482

American (AMR) AF: 0.290 AC: 4432 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 628 AN: 3470

East Asian (EAS) AF: 0.0389 AC: 201 AN: 5168

South Asian (SAS) AF: 0.230 AC: 1106 AN: 4816

European-Finnish (FIN) AF: 0.194 AC: 2059 AN: 10592

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16016 AN: 67982

Other (OTH) AF: 0.240 AC: 507 AN: 2116

Alfa AF: 0.232 Hom.: 6602

Bravo AF: 0.241

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.30
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs4854306; hg19: chr2-433274;