rs1800587

Variant names:

• chr2-112785383-G-A
• rs1800587

Your query was ambiguous. Multiple possible variants found:

• chr2-112785383-G-A
• chr2-112785383-G-C
• chr2-112785383-G-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 0.317 in 152,114 control chromosomes in the GnomAD database, including 7,960 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 0.32 (7960 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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: 0.317 AC: 48202 AN: 151996 Hom.: 7944 Cov.: 33

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.0787

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.317 AC: 48262 AN: 152114 Hom.: 7960 Cov.: 33 AF XY: 0.317 AC XY: 23570 AN XY: 74352

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.0787

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.306

Alfa AF: 0.285 Hom.: 6471

Bravo AF: 0.316

Asia WGS AF: 0.212 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800587; hg19: chr2-113542960;