rs3759125

Variant names:

• chr12-49949825-A-C
• rs3759125

Your query was ambiguous. Multiple possible variants found:

• chr12-49949825-A-C
• chr12-49949825-A-G
• chr12-49949825-A-T

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 0.509 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.516 AC: 21377 AN: 41454

American (AMR) AF: 0.543 AC: 8292 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2218 AN: 3470

East Asian (EAS) AF: 0.629 AC: 3253 AN: 5172

South Asian (SAS) AF: 0.731 AC: 3524 AN: 4824

European-Finnish (FIN) AF: 0.431 AC: 4548 AN: 10560

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32466 AN: 67952

Other (OTH) AF: 0.532 AC: 1123 AN: 2110

Alfa AF: 0.497 Hom.: 78027

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3759125; hg19: chr12-50343608;