rs1863800

chr2-203837937-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.446

Alfa AF: 0.425 Hom.: 4940

Bravo AF: 0.395

Asia WGS AF: 0.455 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.35
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1863800; hg19: chr2-204702660;