2-142206803-T-C

Variant names:

• chr2-142206803-T-C
• rs1523702

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 0.0828 in 152,188 control chromosomes in the GnomAD database, including 639 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 0.083 (639 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 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: 0.0829 AC: 12601 AN: 152070 Hom.: 638 Cov.: 31

Gnomad AFR AF: 0.0517

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0495

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0453

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0674

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

GnomAD4 genome AF: 0.0828 AC: 12600 AN: 152188 Hom.: 639 Cov.: 31 AF XY: 0.0841 AC XY: 6262 AN XY: 74422

African (AFR) AF: 0.0516 AC: 2145 AN: 41556

American (AMR) AF: 0.0495 AC: 756 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0890 AC: 309 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.0449 AC: 217 AN: 4830

European-Finnish (FIN) AF: 0.165 AC: 1747 AN: 10600

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7143 AN: 67948

Other (OTH) AF: 0.0667 AC: 141 AN: 2114

Alfa AF: 0.0893 Hom.: 339

Bravo AF: 0.0744

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.3
DANN	Benign	0.87
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs1523702; hg19: chr2-142964372;