chr2-95574025-A-G

Variant names:

• chr2-95574025-A-G
• rs2320170

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 0.307 in 151,720 control chromosomes in the GnomAD database, including 7,967 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 0.31 (7967 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.85
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.399 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: 0.307 AC: 46555 AN: 151600 Hom.: 7945 Cov.: 31

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.307 AC: 46619 AN: 151720 Hom.: 7967 Cov.: 31 AF XY: 0.309 AC XY: 22914 AN XY: 74118

African (AFR) AF: 0.180 AC: 7449 AN: 41396

American (AMR) AF: 0.407 AC: 6196 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 661 AN: 3466

East Asian (EAS) AF: 0.332 AC: 1708 AN: 5142

South Asian (SAS) AF: 0.195 AC: 935 AN: 4796

European-Finnish (FIN) AF: 0.470 AC: 4947 AN: 10516

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23786 AN: 67874

Other (OTH) AF: 0.279 AC: 586 AN: 2104

Alfa AF: 0.344 Hom.: 2042

Bravo AF: 0.306

Asia WGS AF: 0.252 AC: 873 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.011
DANN	Benign	0.13
PhyloP100		-4.9

Splicing

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

Other links and lift over

dbSNP: rs2320170; hg19: chr2-96239773;