rs13402702

Positions:

• chr2-28957536-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000401723.5(TOGARAM2):​c.-147+839A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,202 control chromosomes in the GnomAD database, including 1,557 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 0.12 (1557 hom., cov: 32)
• Consequence: TOGARAM2 ENST00000401723.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.873

Genes affected

TOGARAM2 (HGNC:33715): (TOG array regulator of axonemal microtubules 2) Predicted to enable microtubule binding activity. Predicted to be involved in mitotic spindle assembly. Predicted to be active in cilium and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TOGARAM2	XM_047443568.1	c.-111+839A>G		intron_variant			XP_047299524.1
TOGARAM2	XM_047443570.1	c.-111+839A>G		intron_variant			XP_047299526.1
TOGARAM2	XM_047443574.1	c.-127+839A>G		intron_variant			XP_047299530.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TOGARAM2	ENST00000401723.5	c.-147+839A>G		intron_variant		5		ENSP00000384897

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18721 AN: 152084 Hom.: 1555 Cov.: 32

Gnomad AFR AF: 0.0311

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0560

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.123 AC: 18723 AN: 152202 Hom.: 1557 Cov.: 32 AF XY: 0.121 AC XY: 9017 AN XY: 74414

Gnomad4 AFR AF: 0.0310

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0568

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.154

Alfa AF: 0.171 Hom.: 3103

Bravo AF: 0.115

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13402702; hg19: chr2-29180402;