Variant chr11-102047596-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_032930.3(CFAP300):c.110+16A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.97 in 1,533,484 control chromosomes in the GnomAD database, including 721,938 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.96 ( 70793 hom., cov: 33)

Exomes 𝑓: 0.97 ( 651145 hom. )

Consequence

CFAP300
NM_032930.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.157

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 11-102047596-A-G is Benign according to our data. Variant chr11-102047596-A-G is described in ClinVar as [Benign]. Clinvar id is 1192590.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
CFAP300	NM_032930.3 linkuse as main transcript	c.110+16A>G	intron_variant	ENST00000434758.7
CFAP300	NM_001195005.2 linkuse as main transcript	c.110+16A>G	intron_variant
CFAP300	NM_001363505.2 linkuse as main transcript	c.110+16A>G	intron_variant
CFAP300	XM_005271713.5 linkuse as main transcript	c.110+16A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP300	ENST00000434758.7 linkuse as main transcript	c.110+16A>G	intron_variant		2	NM_032930.3	P1	Q9BRQ4-1
CFAP300	ENST00000534360.1 linkuse as main transcript	c.110+16A>G	intron_variant		1			Q9BRQ4-3
CFAP300	ENST00000530659.1 linkuse as main transcript	n.129A>G	non_coding_transcript_exon_variant	1/6	1
CFAP300	ENST00000526781.5 linkuse as main transcript	c.110+16A>G	intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.964

AC:

146722

AN:

152206

Hom.:

70737

Cov.:

show subpopulations

Gnomad AFR

AF:

0.939

Gnomad AMI

AF:

0.943

Gnomad AMR

AF:

0.971

Gnomad ASJ

AF:

0.959

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.981

Gnomad FIN

AF:

0.978

Gnomad MID

AF:

0.962

Gnomad NFE

AF:

0.972

Gnomad OTH

AF:

0.960

GnomAD3 exomes

AF:

0.971

AC:

134141

AN:

138130

Hom.:

65142

AF XY:

0.972

AC XY:

72751

AN XY:

74828

show subpopulations

Gnomad AFR exome

AF:

0.936

Gnomad AMR exome

AF:

0.972

Gnomad ASJ exome

AF:

0.949

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.979

Gnomad FIN exome

AF:

0.980

Gnomad NFE exome

AF:

0.969

Gnomad OTH exome

AF:

0.967

GnomAD4 exome

AF:

0.971

AC:

1341102

AN:

1381160

Hom.:

651145

Cov.:

AF XY:

0.971

AC XY:

662055

AN XY:

681722

show subpopulations

Gnomad4 AFR exome

AF:

0.935

Gnomad4 AMR exome

AF:

0.971

Gnomad4 ASJ exome

AF:

0.951

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.980

Gnomad4 FIN exome

AF:

0.976

Gnomad4 NFE exome

AF:

0.971

Gnomad4 OTH exome

AF:

0.969

GnomAD4 genome

AF:

0.964

AC:

146836

AN:

152324

Hom.:

70793

Cov.:

AF XY:

0.965

AC XY:

71852

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.939

Gnomad4 AMR

AF:

0.971

Gnomad4 ASJ

AF:

0.959

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.981

Gnomad4 FIN

AF:

0.978

Gnomad4 NFE

AF:

0.972

Gnomad4 OTH

AF:

0.961

Alfa

AF:

0.968

Hom.:

65319

Bravo

AF:

0.961

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -

Ciliary dyskinesia, primary, 38

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.7

DANN

Benign

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over