chr1-18837989-A-G

Variant names:

• chr1-18837989-A-G
• rs12036097

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;