chr2-203876827-G-A

Variant names:

• chr2-203876827-G-A
• rs231727

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 0.378 in 151,868 control chromosomes in the GnomAD database, including 11,292 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 0.38 (11292 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 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: 0.378 AC: 57351 AN: 151750 Hom.: 11280 Cov.: 31

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.378 AC: 57408 AN: 151868 Hom.: 11292 Cov.: 31 AF XY: 0.385 AC XY: 28556 AN XY: 74204

African (AFR) AF: 0.418 AC: 17296 AN: 41402

American (AMR) AF: 0.393 AC: 5986 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 932 AN: 3470

East Asian (EAS) AF: 0.590 AC: 3052 AN: 5174

South Asian (SAS) AF: 0.281 AC: 1346 AN: 4790

European-Finnish (FIN) AF: 0.485 AC: 5093 AN: 10506

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22600 AN: 67966

Other (OTH) AF: 0.329 AC: 695 AN: 2110

Alfa AF: 0.339 Hom.: 2876

Bravo AF: 0.377

Asia WGS AF: 0.392 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.61
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs231727; hg19: chr2-204741550;