14-103102435-CCG-AGT

Variant names:

• chr14-103102435-CCG-AGT
• NM_001077594.2:c.712_714delCCGinsAGT
• EXOC3L4 p.Pro238Ser

Variant summary

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

The NM_001077594.2(EXOC3L4):​c.712_714delCCGinsAGT​(p.Pro238Ser) 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P238R) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 34)
• Consequence: EXOC3L4 NM_001077594.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.27
• Publications: 0 publications found

Genes affected

EXOC3L4 (HGNC:20120): (exocyst complex component 3 like 4) Predicted to enable SNARE binding activity. Predicted to be involved in exocyst localization and exocytosis. Predicted to be part of exocyst. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001077594.2. 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
	EXOC3L4	NM_001077594.2	MANE Select	c.712_714delCCGinsAGT	p.Pro238Ser	missense	N/A	NP_001071062.1	Q17RC7
	EXOC3L4	NM_001394941.1		c.712_714delCCGinsAGT	p.Pro238Ser	missense	N/A	NP_001381870.1	Q17RC7
	EXOC3L4	NM_001394942.1		c.712_714delCCGinsAGT	p.Pro238Ser	missense	N/A	NP_001381871.1	Q17RC7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EXOC3L4	ENST00000688303.1	MANE Select	c.712_714delCCGinsAGT	p.Pro238Ser	missense	N/A	ENSP00000509130.1	Q17RC7
	EXOC3L4	ENST00000380069.7	TSL:1	c.712_714delCCGinsAGT	p.Pro238Ser	missense	N/A	ENSP00000369409.3	Q17RC7
	EXOC3L4	ENST00000687959.1		c.712_714delCCGinsAGT	p.Pro238Ser	missense	N/A	ENSP00000508483.1	Q17RC7

Frequencies

GnomAD3 genomes Cov.: 34

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

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.3

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: chr14-103568772;