11-102047858-C-G

Variant names:

• chr11-102047858-C-G
• rs767760877
• NM_032930.3:c.154C>G

Variant summary

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

The NM_032930.3(CFAP300):​c.154C>G​(p.Gln52Glu) 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. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CFAP300 NM_032930.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.967
• Publications: 1 publications found

Genes affected

CFAP300 (HGNC:28188): (cilia and flagella associated protein 300) Predicted to be located in cytoplasm and motile cilium. Implicated in primary ciliary dyskinesia 38. [provided by Alliance of Genome Resources, Apr 2022]

CFAP300 Gene-Disease associations (from GenCC):

• ciliary dyskinesia, primary, 38

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Labcorp Genetics (formerly Invitae)
• primary ciliary dyskinesia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

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=0.19164833).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP300	NM_032930.3	c.154C>G	p.Gln52Glu	missense_variant	Exon 2 of 7	ENST00000434758.7	NP_116319.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP300	ENST00000434758.7	c.154C>G	p.Gln52Glu	missense_variant	Exon 2 of 7	2	NM_032930.3	ENSP00000414390.2
CFAP300	ENST00000534360.1	c.154C>G	p.Gln52Glu	missense_variant	Exon 2 of 4	1		ENSP00000435482.1
CFAP300	ENST00000530659.1	n.391C>G		non_coding_transcript_exon_variant	Exon 1 of 6	1
CFAP300	ENST00000526781.5	c.154C>G	p.Gln52Glu	missense_variant	Exon 2 of 6	3		ENSP00000433074.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.072
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	16
DANN	Benign	0.97
DEOGEN2	Benign	0.034	T;.;.
Eigen	Benign	-0.37
Eigen_PC	Benign	-0.23
FATHMM_MKL	Benign	0.46	N
LIST_S2	Benign	0.76	T;T;T
M_CAP	Benign	0.0036	T
MetaRNN	Benign	0.19	T;T;T
MetaSVM	Benign	-0.94	T
PhyloP100		0.97
PROVEAN	Benign	-1.2	N;N;N
REVEL	Benign	0.028
Sift	Benign	0.092	T;T;T
Sift4G	Benign	0.35	T;T;T
Polyphen		0.0090	B;.;.
Vest4		0.29
MutPred		0.49		Gain of helix (P = 0.0425);Gain of helix (P = 0.0425);Gain of helix (P = 0.0425);
MVP		0.22
MPC		0.038
ClinPred		0.26	T
GERP RS		2.3
PromoterAI		0.073	Neutral
Varity_R		0.090
gMVP		0.43
Mutation Taster		=90/10	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs767760877; hg19: chr11-101918589; COSMIC: COSV105939729;