12-51942223-G-T

Variant names:

• chr12-51942223-G-T
• rs10783485

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 0.307 in 152,064 control chromosomes in the GnomAD database, including 9,356 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 0.31 (9356 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 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: 0.308 AC: 46728 AN: 151946 Hom.: 9350 Cov.: 32

Gnomad AFR AF: 0.0880

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.307 AC: 46737 AN: 152064 Hom.: 9356 Cov.: 32 AF XY: 0.315 AC XY: 23406 AN XY: 74328

Gnomad4 AFR AF: 0.0880

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.348

Alfa AF: 0.371 Hom.: 3251

Bravo AF: 0.318

Asia WGS AF: 0.533 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0060
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10783485; hg19: chr12-52336007;