3-36332273-C-T

Variant names:

• chr3-36332273-C-T
• rs1871350

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 0.847 in 152,022 control chromosomes in the GnomAD database, including 54,596 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 0.85 (54596 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 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: 0.847 AC: 128686 AN: 151904 Hom.: 54555 Cov.: 31

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.847 AC: 128784 AN: 152022 Hom.: 54596 Cov.: 31 AF XY: 0.850 AC XY: 63121 AN XY: 74272

African (AFR) AF: 0.832 AC: 34511 AN: 41478

American (AMR) AF: 0.837 AC: 12777 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.873 AC: 3020 AN: 3460

East Asian (EAS) AF: 0.990 AC: 5092 AN: 5146

South Asian (SAS) AF: 0.872 AC: 4196 AN: 4812

European-Finnish (FIN) AF: 0.866 AC: 9164 AN: 10576

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57153 AN: 67966

Other (OTH) AF: 0.836 AC: 1767 AN: 2114

Alfa AF: 0.842 Hom.: 27125

Bravo AF: 0.844

Asia WGS AF: 0.923 AC: 3213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.36
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1871350; hg19: chr3-36373765;