chr12-18899246-A-G

Variant names:

• chr12-18899246-A-G
• rs1873386

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 0.313 in 151,996 control chromosomes in the GnomAD database, including 9,295 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 0.31 (9295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 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: 0.313 AC: 47496 AN: 151876 Hom.: 9284 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.313 AC: 47555 AN: 151996 Hom.: 9295 Cov.: 32 AF XY: 0.317 AC XY: 23536 AN XY: 74312

African (AFR) AF: 0.527 AC: 21815 AN: 41418

American (AMR) AF: 0.373 AC: 5696 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1082 AN: 3468

East Asian (EAS) AF: 0.509 AC: 2620 AN: 5146

South Asian (SAS) AF: 0.230 AC: 1105 AN: 4812

European-Finnish (FIN) AF: 0.185 AC: 1955 AN: 10578

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.181 AC: 12285 AN: 67990

Other (OTH) AF: 0.300 AC: 632 AN: 2110

Alfa AF: 0.238 Hom.: 16525

Bravo AF: 0.342

Asia WGS AF: 0.368 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.70
DANN	Benign	0.52
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1873386; hg19: chr12-19052180;