chr1-18837989-A-G

Variant names:

• chr1-18837989-A-G
• rs12036097

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.426 AC: 17658 AN: 41404

American (AMR) AF: 0.431 AC: 6582 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1514 AN: 3462

East Asian (EAS) AF: 0.553 AC: 2853 AN: 5156

South Asian (SAS) AF: 0.450 AC: 2169 AN: 4818

European-Finnish (FIN) AF: 0.424 AC: 4485 AN: 10584

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.506 AC: 34414 AN: 67962

Other (OTH) AF: 0.467 AC: 988 AN: 2114

Alfa AF: 0.476 Hom.: 7585

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
PhyloP100		-0.75

Splicing

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

Other links and lift over

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