2-19901729-GGC-TGG

Variant names:

• chr2-19901729-GGC-TGG
• NM_001008237.3:c.124_126delGCCinsCCA
• TTC32 p.Ala42Pro

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001008237.3(TTC32):​c.124_126delGCCinsCCA​(p.Ala42Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A42T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: TTC32 NM_001008237.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 0 publications found

Genes affected

TTC32 (HGNC:32954): (tetratricopeptide repeat domain 32)

TTC32-DT (HGNC:55236): (TTC32 divergent transcript)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001008237.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC32	NM_001008237.3	MANE Select	c.124_126delGCCinsCCA	p.Ala42Pro	missense	N/A	NP_001008238.1	Q5I0X7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC32	ENST00000333610.4	TSL:1 MANE Select	c.124_126delGCCinsCCA	p.Ala42Pro	missense	N/A	ENSP00000333018.3	Q5I0X7
	TTC32	ENST00000916781.1		c.124_126delGCCinsCCA	p.Ala42Pro	missense	N/A	ENSP00000586840.1
	TTC32	ENST00000402414.1	TSL:5	c.124_126delGCCinsCCA	p.Ala42Pro	missense	N/A	ENSP00000385708.1	B5MCJ1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr2-20101490;