3-36332273-C-T

Position:

• chr3-36332273-C-T

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 0.847 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.873

Gnomad4 EAS AF: 0.990

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.836

Alfa AF: 0.841 Hom.: 24075

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1871350; hg19: chr3-36373765;