chr2-25345310-A-G

Variant names:

• chr2-25345310-A-G
• rs36012910

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 0.0393 in 152,346 control chromosomes in the GnomAD database, including 156 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 0.039 (156 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0731 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: 0.0394 AC: 5994 AN: 152228 Hom.: 156 Cov.: 32

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0277

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.0380

Gnomad SAS AF: 0.0798

Gnomad FIN AF: 0.0469

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0485

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0393 AC: 5994 AN: 152346 Hom.: 156 Cov.: 32 AF XY: 0.0394 AC XY: 2935 AN XY: 74496

African (AFR) AF: 0.0182 AC: 756 AN: 41584

American (AMR) AF: 0.0277 AC: 424 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0859 AC: 298 AN: 3470

East Asian (EAS) AF: 0.0379 AC: 197 AN: 5196

South Asian (SAS) AF: 0.0797 AC: 385 AN: 4832

European-Finnish (FIN) AF: 0.0469 AC: 498 AN: 10618

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0485 AC: 3301 AN: 68020

Other (OTH) AF: 0.0364 AC: 77 AN: 2114

Alfa AF: 0.0178 Hom.: 6

Bravo AF: 0.0359

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.55
DANN	Benign	0.39
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs36012910; hg19: chr2-25568179;