2-203837937-C-T

Variant names:

• chr2-203837937-C-T
• rs1863800

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 0.394 in 151,960 control chromosomes in the GnomAD database, including 12,056 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 0.39 (12056 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59784 AN: 151842 Hom.: 12057 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.394 AC: 59798 AN: 151960 Hom.: 12056 Cov.: 32 AF XY: 0.391 AC XY: 29016 AN XY: 74264

African (AFR) AF: 0.349 AC: 14461 AN: 41410

American (AMR) AF: 0.419 AC: 6405 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1807 AN: 3472

East Asian (EAS) AF: 0.245 AC: 1271 AN: 5178

South Asian (SAS) AF: 0.600 AC: 2893 AN: 4820

European-Finnish (FIN) AF: 0.303 AC: 3198 AN: 10552

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28283 AN: 67934

Other (OTH) AF: 0.446 AC: 944 AN: 2116

Alfa AF: 0.420 Hom.: 6696

Bravo AF: 0.395

Asia WGS AF: 0.455 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.39
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1863800; hg19: chr2-204702660;