chr3-36310872-A-C

Variant names:

• chr3-36310872-A-C
• rs2046000

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 0.828 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.828 AC: 34368 AN: 41532

American (AMR) AF: 0.784 AC: 11963 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3020 AN: 3470

East Asian (EAS) AF: 0.779 AC: 4030 AN: 5174

South Asian (SAS) AF: 0.791 AC: 3814 AN: 4822

European-Finnish (FIN) AF: 0.870 AC: 9218 AN: 10596

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56821 AN: 67986

Other (OTH) AF: 0.816 AC: 1727 AN: 2116

Alfa AF: 0.836 Hom.: 131344

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
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs2046000; hg19: chr3-36352364;