rs12036097

chr1-18837989-A-G

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 0.469 in 151,990 control chromosomes in the GnomAD database, including 16,965 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 0.47 (16965 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 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: 0.469 AC: 71263 AN: 151872 Hom.: 16968 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.469 AC: 71274 AN: 151990 Hom.: 16965 Cov.: 32 AF XY: 0.464 AC XY: 34461 AN XY: 74308

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.467

Alfa AF: 0.475 Hom.: 6156

Bravo AF: 0.468

Asia WGS AF: 0.481 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.76
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12036097; hg19: chr1-19164483; COSMIC: COSV64744146;