chr2-238205234-G-A

Variant names:

• chr2-238205234-G-A
• rs34795319

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 0.276 in 152,024 control chromosomes in the GnomAD database, including 6,163 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 0.28 (6163 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.353 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: 0.276 AC: 41904 AN: 151906 Hom.: 6158 Cov.: 33

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.276 AC: 41919 AN: 152024 Hom.: 6163 Cov.: 33 AF XY: 0.276 AC XY: 20488 AN XY: 74296

African (AFR) AF: 0.177 AC: 7347 AN: 41496

American (AMR) AF: 0.253 AC: 3857 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3472

East Asian (EAS) AF: 0.210 AC: 1086 AN: 5168

South Asian (SAS) AF: 0.367 AC: 1771 AN: 4822

European-Finnish (FIN) AF: 0.333 AC: 3512 AN: 10556

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22595 AN: 67932

Other (OTH) AF: 0.270 AC: 571 AN: 2112

Alfa AF: 0.181 Hom.: 396

Bravo AF: 0.266

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.3
DANN	Benign	0.32
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs34795319; hg19: chr2-239113875;