chr2-96562302-G-A

Variant names:

• chr2-96562302-G-A
• rs4907240

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 0.239 in 152,124 control chromosomes in the GnomAD database, including 5,874 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 0.24 (5874 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36327 AN: 152006 Hom.: 5859 Cov.: 32

Gnomad AFR AF: 0.0744

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.239 AC: 36359 AN: 152124 Hom.: 5874 Cov.: 32 AF XY: 0.245 AC XY: 18210 AN XY: 74366

African (AFR) AF: 0.0744 AC: 3087 AN: 41500

American (AMR) AF: 0.398 AC: 6085 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3470

East Asian (EAS) AF: 0.439 AC: 2274 AN: 5176

South Asian (SAS) AF: 0.645 AC: 3106 AN: 4812

European-Finnish (FIN) AF: 0.194 AC: 2058 AN: 10594

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17745 AN: 67970

Other (OTH) AF: 0.295 AC: 620 AN: 2104

Alfa AF: 0.263 Hom.: 12304

Bravo AF: 0.245

Asia WGS AF: 0.541 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.61
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4907240; hg19: chr2-97228039;