chr2-203705277-G-T

Variant names:

• chr2-203705277-G-T
• rs1879877

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 0.264 in 151,998 control chromosomes in the GnomAD database, including 5,723 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 0.26 (5723 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.561 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: 0.264 AC: 40033 AN: 151880 Hom.: 5702 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.264 AC: 40114 AN: 151998 Hom.: 5723 Cov.: 32 AF XY: 0.265 AC XY: 19655 AN XY: 74294

African (AFR) AF: 0.286 AC: 11857 AN: 41434

American (AMR) AF: 0.293 AC: 4478 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1046 AN: 3470

East Asian (EAS) AF: 0.578 AC: 2985 AN: 5164

South Asian (SAS) AF: 0.165 AC: 794 AN: 4808

European-Finnish (FIN) AF: 0.216 AC: 2284 AN: 10562

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15667 AN: 67964

Other (OTH) AF: 0.288 AC: 609 AN: 2114

Alfa AF: 0.244 Hom.: 13185

Bravo AF: 0.277

Asia WGS AF: 0.333 AC: 1160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.5
DANN	Benign	0.76
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs1879877; hg19: chr2-204570000;