12-124776099-A-G

Variant names:

• chr12-124776099-A-G
• rs838878

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 0.599 in 152,102 control chromosomes in the GnomAD database, including 29,215 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 0.60 (29215 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 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: 0.599 AC: 91070 AN: 151984 Hom.: 29207 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.599 AC: 91113 AN: 152102 Hom.: 29215 Cov.: 33 AF XY: 0.598 AC XY: 44495 AN XY: 74358

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.648

Alfa AF: 0.683 Hom.: 73202

Bravo AF: 0.603

Asia WGS AF: 0.701 AC: 2438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs838878; hg19: chr12-125260645;