rs3126184

Variant names:

• chr14-49905817-T-C
• rs3126184

Your query was ambiguous. Multiple possible variants found:

• chr14-49905817-T-C
• chr14-49905817-T-G

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 0.871 in 152,220 control chromosomes in the GnomAD database, including 57,836 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 0.87 (57836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 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: 0.871 AC: 132481 AN: 152102 Hom.: 57785 Cov.: 32

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.871 AC: 132592 AN: 152220 Hom.: 57836 Cov.: 32 AF XY: 0.873 AC XY: 64976 AN XY: 74418

African (AFR) AF: 0.829 AC: 34426 AN: 41524

American (AMR) AF: 0.905 AC: 13839 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3000 AN: 3468

East Asian (EAS) AF: 0.939 AC: 4874 AN: 5188

South Asian (SAS) AF: 0.916 AC: 4425 AN: 4832

European-Finnish (FIN) AF: 0.871 AC: 9217 AN: 10588

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59888 AN: 68018

Other (OTH) AF: 0.868 AC: 1833 AN: 2112

Alfa AF: 0.878 Hom.: 178978

Bravo AF: 0.871

Asia WGS AF: 0.925 AC: 3218 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	6.8
DANN	Benign	0.68
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs3126184; hg19: chr14-50372535;