rs2046000

Positions:

• chr3-36310872-A-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;