rs231804

Variant names:

• chr2-203843923-C-T
• rs231804

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 0.6 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
• Publications: 19 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 (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

African (AFR) AF: 0.628 AC: 25928 AN: 41272

American (AMR) AF: 0.580 AC: 8823 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1683 AN: 3464

East Asian (EAS) AF: 0.753 AC: 3888 AN: 5160

South Asian (SAS) AF: 0.405 AC: 1948 AN: 4808

European-Finnish (FIN) AF: 0.692 AC: 7244 AN: 10466

Middle Eastern (MID) AF: 0.469 AC: 135 AN: 288

European-Non Finnish (NFE) AF: 0.584 AC: 39644 AN: 67918

Other (OTH) AF: 0.552 AC: 1156 AN: 2096

Alfa AF: 0.572 Hom.: 17753

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
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs231804; hg19: chr2-204708646;