rs12090585

Variant names:

• chr1-162068986-G-A
• rs12090585

Your query was ambiguous. Multiple possible variants found:

• chr1-162068986-G-A
• chr1-162068986-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 0.32 in 151,990 control chromosomes in the GnomAD database, including 8,235 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 (8235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.609 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: 0.320 AC: 48622 AN: 151872 Hom.: 8233 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.320 AC: 48645 AN: 151990 Hom.: 8235 Cov.: 32 AF XY: 0.328 AC XY: 24346 AN XY: 74276

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.321

Alfa AF: 0.314 Hom.: 4199

Bravo AF: 0.308

Asia WGS AF: 0.574 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12090585; hg19: chr1-162038776;