11-102047811-C-A

Position:

• chr11-102047811-C-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_032930.3(CFAP300):​c.111-4C>A variant causes a splice region, splice polypyrimidine tract, intron 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. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CFAP300 NM_032930.3 splice_region, splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.00003005
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.106

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 Likely_benign. Variant got -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BP6: Variant 11-102047811-C-A is Benign according to our data. Variant chr11-102047811-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2755591.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP300	NM_032930.3	c.111-4C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000434758.7
CFAP300	NM_001195005.2	c.111-4C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
CFAP300	NM_001363505.2	c.111-4C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
CFAP300	XM_005271713.5	c.111-4C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP300	ENST00000434758.7	c.111-4C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		2	NM_032930.3	P1
CFAP300	ENST00000534360.1	c.111-4C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1
CFAP300	ENST00000530659.1	n.344C>A		non_coding_transcript_exon_variant	1/6	1
CFAP300	ENST00000526781.5	c.111-4C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Sep 06, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	5.7
DANN	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000030
dbscSNV1_RF	Benign	0.012
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: chr11-101918542;