chr11-102047811-C-A

Variant names:

• chr11-102047811-C-A
• NM_032930.3:c.111-4C>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, 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, 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 rank	MANE	Protein	UniProt
CFAP300	NM_032930.3	c.111-4C>A		splice_region_variant, intron_variant	Intron 1 of 6	ENST00000434758.7	NP_116319.2
CFAP300	NM_001363505.2	c.111-4C>A		splice_region_variant, intron_variant	Intron 1 of 5		NP_001350434.1
CFAP300	NM_001195005.2	c.111-4C>A		splice_region_variant, intron_variant	Intron 1 of 3		NP_001181934.1
CFAP300	XM_005271713.5	c.111-4C>A		splice_region_variant, 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.111-4C>A		splice_region_variant, intron_variant	Intron 1 of 6	2	NM_032930.3	ENSP00000414390.2
CFAP300	ENST00000534360.1	c.111-4C>A		splice_region_variant, intron_variant	Intron 1 of 3	1		ENSP00000435482.1
CFAP300	ENST00000530659.1	n.344C>A		non_coding_transcript_exon_variant	Exon 1 of 6	1
CFAP300	ENST00000526781.5	c.111-4C>A		splice_region_variant, intron_variant	Intron 1 of 5	3		ENSP00000433074.1

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

Sep 06, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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;