rs2184588

Variant names:

• chr1-89342171-G-A
• rs2184588

Your query was ambiguous. Multiple possible variants found:

• chr1-89342171-G-A
• chr1-89342171-G-C

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 0.0885 in 152,126 control chromosomes in the GnomAD database, including 1,105 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 0.088 (1105 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 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: 0.0885 AC: 13446 AN: 152008 Hom.: 1106 Cov.: 32

Gnomad AFR AF: 0.0924

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0447

Gnomad OTH AF: 0.0871

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

GnomAD4 genome AF: 0.0885 AC: 13457 AN: 152126 Hom.: 1105 Cov.: 32 AF XY: 0.0947 AC XY: 7039 AN XY: 74366

African (AFR) AF: 0.0922 AC: 3828 AN: 41500

American (AMR) AF: 0.139 AC: 2124 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3472

East Asian (EAS) AF: 0.472 AC: 2431 AN: 5148

South Asian (SAS) AF: 0.124 AC: 600 AN: 4824

European-Finnish (FIN) AF: 0.106 AC: 1123 AN: 10582

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0447 AC: 3039 AN: 67998

Other (OTH) AF: 0.0914 AC: 193 AN: 2112

Alfa AF: 0.0719 Hom.: 362

Bravo AF: 0.0944

Asia WGS AF: 0.286 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2184588; hg19: chr1-89807854;