chr2-120352302-G-A

Variant names:

• chr2-120352302-G-A
• rs10183524

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 0.0843 in 152,170 control chromosomes in the GnomAD database, including 842 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 0.084 (842 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 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: 0.0842 AC: 12809 AN: 152052 Hom.: 835 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0496

Gnomad ASJ AF: 0.0534

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0419

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0402

Gnomad OTH AF: 0.0623

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

GnomAD4 genome AF: 0.0843 AC: 12834 AN: 152170 Hom.: 842 Cov.: 33 AF XY: 0.0867 AC XY: 6453 AN XY: 74412

African (AFR) AF: 0.162 AC: 6718 AN: 41520

American (AMR) AF: 0.0495 AC: 757 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0534 AC: 185 AN: 3464

East Asian (EAS) AF: 0.168 AC: 868 AN: 5176

South Asian (SAS) AF: 0.200 AC: 960 AN: 4804

European-Finnish (FIN) AF: 0.0419 AC: 445 AN: 10610

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0402 AC: 2733 AN: 67980

Other (OTH) AF: 0.0659 AC: 139 AN: 2110

Alfa AF: 0.0699 Hom.: 184

Bravo AF: 0.0843

Asia WGS AF: 0.229 AC: 795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.041
DANN	Benign	0.88
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10183524; hg19: chr2-121109878;