rs2184588

chr1-89342171-G-Achr1-89342171-G-C

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 0.0885 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0922

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0447

Gnomad4 OTH AF: 0.0914

Alfa AF: 0.0739 Hom.: 330

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2184588; hg19: chr1-89807854;