12-33053704-T-G

Variant names:

• chr12-33053704-T-G
• rs11052413

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 152,068 control chromosomes in the GnomAD database, including 27,389 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 (27389 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 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: 0.584 AC: 88705 AN: 151950 Hom.: 27343 Cov.: 32

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.584 AC: 88809 AN: 152068 Hom.: 27389 Cov.: 32 AF XY: 0.586 AC XY: 43588 AN XY: 74338

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.577

Alfa AF: 0.545 Hom.: 2964

Bravo AF: 0.594

Asia WGS AF: 0.752 AC: 2607 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.96
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11052413; hg19: chr12-33206638;