rs231804

Variant names:

• chr2-203843923-C-T
• rs231804

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 0.6 in 151,602 control chromosomes in the GnomAD database, including 27,589 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 0.60 (27589 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

ACMG classification

Verdict is Benign. Variant got -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 = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.600 AC: 90873 AN: 151484 Hom.: 27544 Cov.: 29

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.600 AC: 90975 AN: 151602 Hom.: 27589 Cov.: 29 AF XY: 0.603 AC XY: 44636 AN XY: 74050

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.552

Alfa AF: 0.572 Hom.: 16465

Bravo AF: 0.597

Asia WGS AF: 0.545 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs231804; hg19: chr2-204708646;