rs3759125

chr12-49949825-A-Cchr12-49949825-A-Gchr12-49949825-A-T

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 0.509 in 152,022 control chromosomes in the GnomAD database, including 19,974 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 0.51 (19974 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77365 AN: 151904 Hom.: 19945 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.509 AC: 77429 AN: 152022 Hom.: 19974 Cov.: 32 AF XY: 0.511 AC XY: 37991 AN XY: 74302

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.532

Alfa AF: 0.492 Hom.: 32429

Bravo AF: 0.512

Asia WGS AF: 0.678 AC: 2356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.18
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3759125; hg19: chr12-50343608;