2-229346530-A-G

Variant names:

• chr2-229346530-A-G
• rs4972894

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 0.22 in 152,152 control chromosomes in the GnomAD database, including 4,268 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 0.22 (4268 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 10 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 = 0.511 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: 0.220 AC: 33379 AN: 152034 Hom.: 4256 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.220 AC: 33425 AN: 152152 Hom.: 4268 Cov.: 32 AF XY: 0.221 AC XY: 16427 AN XY: 74378

African (AFR) AF: 0.271 AC: 11241 AN: 41496

American (AMR) AF: 0.316 AC: 4825 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 578 AN: 3470

East Asian (EAS) AF: 0.527 AC: 2715 AN: 5148

South Asian (SAS) AF: 0.271 AC: 1304 AN: 4814

European-Finnish (FIN) AF: 0.113 AC: 1201 AN: 10612

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.162 AC: 11005 AN: 68016

Other (OTH) AF: 0.225 AC: 476 AN: 2114

Alfa AF: 0.212 Hom.: 645

Bravo AF: 0.236

Asia WGS AF: 0.405 AC: 1405 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	6.1
DANN	Benign	0.61
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs4972894; hg19: chr2-230211246;