20-24584970-GCA-ACC

Variant names:

• chr20-24584970-GCA-ACC
• NM_024893.3:c.595_597delGCAinsACC
• SYNDIG1 p.Ala199Thr

Variant summary

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

The NM_024893.3(SYNDIG1):​c.595_597delGCAinsACC​(p.Ala199Thr) variant causes a missense change. 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: SYNDIG1 NM_024893.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.66
• Publications: 0 publications found

Genes affected

SYNDIG1 (HGNC:15885): (synapse differentiation inducing 1) This gene encodes a protein that belongs to the interferon-induced transmembrane family of proteins. A similar protein in rat is thought to regulate the development of excitatory synapses. [provided by RefSeq, Jul 2013]

SYNDIG1 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024893.3. 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
	SYNDIG1	NM_024893.3	MANE Select	c.595_597delGCAinsACC	p.Ala199Thr	missense	N/A	NP_079169.1	Q9H7V2
	SYNDIG1	NM_001323606.2		c.595_597delGCAinsACC	p.Ala199Thr	missense	N/A	NP_001310535.1	Q9H7V2
	SYNDIG1	NM_001323607.2		c.595_597delGCAinsACC	p.Ala199Thr	missense	N/A	NP_001310536.1	Q9H7V2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYNDIG1	ENST00000376862.4	TSL:1 MANE Select	c.595_597delGCAinsACC	p.Ala199Thr	missense	N/A	ENSP00000366058.3	Q9H7V2
	SYNDIG1	ENST00000892834.1		c.595_597delGCAinsACC	p.Ala199Thr	missense	N/A	ENSP00000562893.1
	SYNDIG1	ENST00000892835.1		c.595_597delGCAinsACC	p.Ala199Thr	missense	N/A	ENSP00000562894.1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.7

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: chr20-24565606;