12-124776099-A-G

Variant names:

• chr12-124776099-A-G
• rs838878

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 0.599 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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.354 AC: 14670 AN: 41474

American (AMR) AF: 0.738 AC: 11295 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2261 AN: 3468

East Asian (EAS) AF: 0.851 AC: 4413 AN: 5184

South Asian (SAS) AF: 0.602 AC: 2901 AN: 4816

European-Finnish (FIN) AF: 0.595 AC: 6284 AN: 10568

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47017 AN: 67972

Other (OTH) AF: 0.648 AC: 1370 AN: 2114

Alfa AF: 0.670 Hom.: 155834

Bravo AF: 0.603

Asia WGS AF: 0.701 AC: 2438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.54
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs838878; hg19: chr12-125260645;