11-36636083-C-G

Variant names:

• chr11-36636083-C-G
• NM_138787.4:c.324C>G
• IFTAP p.Asp108Glu

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_138787.4(IFTAP):​c.324C>G​(p.Asp108Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. 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: 32)
• Consequence: IFTAP NM_138787.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 0 publications found

Genes affected

IFTAP (HGNC:25142): (intraflagellar transport associated protein) This gene encodes a protein that was identified as a cellular interacting partner of non-structural protein 10 of the severe acute respiratory syndrome coronavirus (SARS-CoV). The encoded protein may function as a negative regulator of transcription. There is a pseudogene for this gene on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013]

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.13815266).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138787.4. 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
	IFTAP	NM_138787.4	MANE Select	c.324C>G	p.Asp108Glu	missense	Exon 4 of 6	NP_620142.2
	IFTAP	NM_001276722.2		c.324C>G	p.Asp108Glu	missense	Exon 4 of 6	NP_001263651.1	Q86VG3-1
	IFTAP	NM_001276723.2		c.324C>G	p.Asp108Glu	missense	Exon 4 of 6	NP_001263652.1	Q86VG3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFTAP	ENST00000334307.10	TSL:1 MANE Select	c.324C>G	p.Asp108Glu	missense	Exon 4 of 6	ENSP00000334848.5	Q86VG3-1
	IFTAP	ENST00000347206.8	TSL:1	c.137-11933C>G		intron	N/A	ENSP00000299442.6	Q86VG3-2
	IFTAP	ENST00000446510.6	TSL:5	c.324C>G	p.Asp108Glu	missense	Exon 4 of 6	ENSP00000403937.3	Q86VG3-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.27
BayesDel_addAF	Benign	-0.052	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	13
DANN	Uncertain	0.99
DEOGEN2	Benign	0.12	T
Eigen	Benign	-0.15
Eigen_PC	Benign	-0.32
FATHMM_MKL	Benign	0.22	N
LIST_S2	Benign	0.58	T
M_CAP	Benign	0.010	T
MetaRNN	Benign	0.14	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Uncertain	2.1	M
PhyloP100		0.21
PROVEAN	Uncertain	-3.0	D
REVEL	Benign	0.091
Sift	Benign	0.21	T
Sift4G	Uncertain	0.014	D
Varity_R		0.12
gMVP		0.041
Mutation Taster		=97/3	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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: chr11-36657633;