rs3759178

Variant names:

• chr12-51905475-G-T
• rs3759178

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 0.6 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.600 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

African (AFR) AF: 0.525 AC: 21760 AN: 41444

American (AMR) AF: 0.563 AC: 8599 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2220 AN: 3468

East Asian (EAS) AF: 0.799 AC: 4121 AN: 5156

South Asian (SAS) AF: 0.635 AC: 3059 AN: 4818

European-Finnish (FIN) AF: 0.670 AC: 7084 AN: 10576

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42353 AN: 67994

Other (OTH) AF: 0.614 AC: 1298 AN: 2114

Alfa AF: 0.615 Hom.: 45356

Bravo AF: 0.589

Asia WGS AF: 0.695 AC: 2418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.60
DANN	Benign	0.80
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs3759178; hg19: chr12-52299259;