rs3759178

Variant names:

• chr12-51905475-G-T
• rs3759178

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 0.6 in 152,052 control chromosomes in the GnomAD database, including 27,704 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 (27704 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 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: 0.600 AC: 91155 AN: 151934 Hom.: 27699 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.600 AC: 91200 AN: 152052 Hom.: 27704 Cov.: 32 AF XY: 0.602 AC XY: 44756 AN XY: 74322

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.614

Alfa AF: 0.615 Hom.: 38157

Bravo AF: 0.589

Asia WGS AF: 0.695 AC: 2418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.60
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3759178; hg19: chr12-52299259;