chr2-203879374-A-T

Variant names:

• chr2-203879374-A-T
• rs231730

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 152,166 control chromosomes in the GnomAD database, including 49,582 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 (49582 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• 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: 122609 AN: 152048 Hom.: 49548 Cov.: 33

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.806 AC: 122697 AN: 152166 Hom.: 49582 Cov.: 33 AF XY: 0.810 AC XY: 60214 AN XY: 74384

African (AFR) AF: 0.779 AC: 32314 AN: 41504

American (AMR) AF: 0.845 AC: 12927 AN: 15294

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

East Asian (EAS) AF: 0.884 AC: 4578 AN: 5180

South Asian (SAS) AF: 0.900 AC: 4346 AN: 4828

European-Finnish (FIN) AF: 0.840 AC: 8883 AN: 10574

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

European-Non Finnish (NFE) AF: 0.798 AC: 54274 AN: 67994

Other (OTH) AF: 0.802 AC: 1695 AN: 2114

Alfa AF: 0.756 Hom.: 2321

Bravo AF: 0.803

Asia WGS AF: 0.885 AC: 3075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.5
DANN	Benign	0.83
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs231730; hg19: chr2-204744097;