rs2046000

Variant names:

• chr3-36310872-A-C
• rs2046000

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 0.828 in 152,164 control chromosomes in the GnomAD database, including 52,283 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 0.83 (52283 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.83 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: 0.828 AC: 125969 AN: 152046 Hom.: 52245 Cov.: 33

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.828 AC: 126062 AN: 152164 Hom.: 52283 Cov.: 33 AF XY: 0.829 AC XY: 61686 AN XY: 74376

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.870

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.816

Alfa AF: 0.837 Hom.: 81871

Bravo AF: 0.823

Asia WGS AF: 0.805 AC: 2799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2046000; hg19: chr3-36352364;