chr2-203879807-C-T

Variant names:

• chr2-203879807-C-T
• rs231731

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 0.806 in 152,202 control chromosomes in the GnomAD database, including 49,539 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 0.81 (49539 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 8 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 (SAS) allele frequency at 95% confidence interval = 0.878 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: 0.806 AC: 122579 AN: 152082 Hom.: 49502 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.802

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

GnomAD4 genome AF: 0.806 AC: 122671 AN: 152202 Hom.: 49539 Cov.: 32 AF XY: 0.809 AC XY: 60219 AN XY: 74412

African (AFR) AF: 0.777 AC: 32252 AN: 41506

American (AMR) AF: 0.845 AC: 12925 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2717 AN: 3472

East Asian (EAS) AF: 0.883 AC: 4572 AN: 5176

South Asian (SAS) AF: 0.901 AC: 4350 AN: 4830

European-Finnish (FIN) AF: 0.841 AC: 8901 AN: 10584

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54298 AN: 68018

Other (OTH) AF: 0.803 AC: 1695 AN: 2112

Alfa AF: 0.799 Hom.: 6910

Bravo AF: 0.803

Asia WGS AF: 0.885 AC: 3077 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	2.2
DANN	Benign	0.61
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs231731; hg19: chr2-204744530;