rs12093699

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;