12-18917759-G-T

Position:

• chr12-18917759-G-T

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 0.249 in 152,026 control chromosomes in the GnomAD database, including 5,854 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 0.25 (5854 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 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: 0.249 AC: 37856 AN: 151908 Hom.: 5845 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.249 AC: 37900 AN: 152026 Hom.: 5854 Cov.: 32 AF XY: 0.255 AC XY: 18955 AN XY: 74340

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.252

Alfa AF: 0.180 Hom.: 2565

Bravo AF: 0.274

Asia WGS AF: 0.358 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.92
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12810703; hg19: chr12-19070693;