rs12093699

Variant names:

• chr1-159678198-G-A
• rs12093699

Your query was ambiguous. Multiple possible variants found:

• chr1-159678198-G-A
• chr1-159678198-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 0.303 in 151,942 control chromosomes in the GnomAD database, including 7,213 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 0.30 (7213 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.323 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: 0.303 AC: 46067 AN: 151824 Hom.: 7208 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.303 AC: 46101 AN: 151942 Hom.: 7213 Cov.: 32 AF XY: 0.302 AC XY: 22425 AN XY: 74282

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.0558

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.292

Alfa AF: 0.299 Hom.: 15111

Bravo AF: 0.306

Asia WGS AF: 0.157 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12093699; hg19: chr1-159647988;