chr12-114554363-G-A

Position:

• chr12-114554363-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.573 in 151,912 control chromosomes in the GnomAD database, including 25,120 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 0.57 (25120 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 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: 0.573 AC: 86974 AN: 151792 Hom.: 25097 Cov.: 31

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.573 AC: 87046 AN: 151912 Hom.: 25120 Cov.: 31 AF XY: 0.570 AC XY: 42315 AN XY: 74246

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.583

Alfa AF: 0.599 Hom.: 20785

Bravo AF: 0.578

Asia WGS AF: 0.538 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	13
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs857748; hg19: chr12-114992168;