12-18873148-G-C

Position:

• chr12-18873148-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 0.584 in 151,994 control chromosomes in the GnomAD database, including 31,034 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 0.58 (31034 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88701 AN: 151876 Hom.: 31038 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.584 AC: 88700 AN: 151994 Hom.: 31034 Cov.: 32 AF XY: 0.583 AC XY: 43278 AN XY: 74286

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.609

Alfa AF: 0.596 Hom.: 2488

Bravo AF: 0.546

Asia WGS AF: 0.594 AC: 2065 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726391; hg19: chr12-19026082;