2-105236375-A-G

Variant names:

• chr2-105236375-A-G
• rs1545122

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 0.831 in 152,130 control chromosomes in the GnomAD database, including 52,794 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 0.83 (52794 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.831 AC: 126316 AN: 152012 Hom.: 52749 Cov.: 31

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.831 AC: 126416 AN: 152130 Hom.: 52794 Cov.: 31 AF XY: 0.830 AC XY: 61726 AN XY: 74352

African (AFR) AF: 0.848 AC: 35182 AN: 41500

American (AMR) AF: 0.863 AC: 13199 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2864 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5156 AN: 5172

South Asian (SAS) AF: 0.922 AC: 4444 AN: 4822

European-Finnish (FIN) AF: 0.710 AC: 7495 AN: 10550

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55337 AN: 68008

Other (OTH) AF: 0.829 AC: 1746 AN: 2106

Alfa AF: 0.821 Hom.: 80877

Bravo AF: 0.841

Asia WGS AF: 0.942 AC: 3276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	15
DANN	Benign	0.73
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs1545122; hg19: chr2-105852832; COSMIC: COSV60087780;