11-102047595-CA-TG

Variant names:

• chr11-102047595-CA-TG
• NM_032930.3:c.110+15_110+16delCAinsTG

Variant summary

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

The NM_032930.3(CFAP300):​c.110+15_110+16delCAinsTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CFAP300 NM_032930.3 intron
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.475

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP300	NM_032930.3	c.110+15_110+16delCAinsTG		intron_variant	Intron 1 of 6	ENST00000434758.7	NP_116319.2
CFAP300	NM_001363505.2	c.110+15_110+16delCAinsTG		intron_variant	Intron 1 of 5		NP_001350434.1
CFAP300	NM_001195005.2	c.110+15_110+16delCAinsTG		intron_variant	Intron 1 of 3		NP_001181934.1
CFAP300	XM_005271713.5	c.110+15_110+16delCAinsTG		intron_variant	Intron 1 of 5		XP_005271770.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP300	ENST00000434758.7	c.110+15_110+16delCAinsTG		intron_variant	Intron 1 of 6	2	NM_032930.3	ENSP00000414390.2
CFAP300	ENST00000534360.1	c.110+15_110+16delCAinsTG		intron_variant	Intron 1 of 3	1		ENSP00000435482.1
CFAP300	ENST00000530659.1	n.128_129delCAinsTG		non_coding_transcript_exon_variant	Exon 1 of 6	1
CFAP300	ENST00000526781.5	c.110+15_110+16delCAinsTG		intron_variant	Intron 1 of 5	3		ENSP00000433074.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Sep 03, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 1 of the C11orf70 gene. It does not directly change the encoded amino acid sequence of the C11orf70 protein. Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This variant has not been reported in the literature in individuals affected with C11orf70-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the effect of this variant on mRNA splicing is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Splicing

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: chr11-101918326;