2-169645896-T-A

Position:

• chr2-169645896-T-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001085447.2(CFAP210):​c.1604A>T​(p.Gln535Leu) 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. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CFAP210 NM_001085447.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.68

Genes affected

CFAP210 (HGNC:25064): (cilia and flagella associated protein 210)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.13604128).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP210	NM_001085447.2	c.1604A>T	p.Gln535Leu	missense_variant	9/9	ENST00000447353.6	NP_001078916.1
CFAP210	XM_047443326.1	c.1532A>T	p.Gln511Leu	missense_variant	10/10		XP_047299282.1
CFAP210	XM_011510590.2	c.1361A>T	p.Gln454Leu	missense_variant	9/9		XP_011508892.1
CFAP210	XM_047443327.1	c.1307A>T	p.Gln436Leu	missense_variant	8/8		XP_047299283.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP210	ENST00000447353.6	c.1604A>T	p.Gln535Leu	missense_variant	9/9	1	NM_001085447.2	ENSP00000391504.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 08, 2023

The c.1604A>T (p.Q535L) alteration is located in exon 9 (coding exon 9) of the CCDC173 gene. This alteration results from a A to T substitution at nucleotide position 1604, causing the glutamine (Q) at amino acid position 535 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	17
DANN	Benign	0.89
DEOGEN2	Benign	0.0074	T
Eigen	Benign	-0.21
Eigen_PC	Benign	-0.14
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Benign	0.57	T
M_CAP	Benign	0.0078	T
MetaRNN	Benign	0.14	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.4	M
MutationTaster	Benign	0.99	N
PrimateAI	Benign	0.22	T
PROVEAN	Uncertain	-2.4	N
REVEL	Benign	0.024
Sift	Benign	0.084	T
Sift4G	Uncertain	0.022	D
Polyphen		0.36	B
Vest4		0.30
MutPred		0.30		Loss of disorder (P = 0.0321);
MVP		0.20
MPC		0.063
ClinPred		0.35	T
GERP RS		3.5
Varity_R		0.12
gMVP		0.099

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-170502406;