Variant 21-32602012-G-A 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 ENST00000382549.8(CFAP298):c.*1077C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0808 in 1,308,542 control chromosomes in the GnomAD database, including 5,742 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1614 hom., cov: 32)

Exomes 𝑓: 0.076 ( 4128 hom. )

Consequence

CFAP298
ENST00000382549.8 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.01

Variant links:

Genes affected

CFAP298 (HGNC:1301): (cilia and flagella associated protein 298) This gene encodes a protein that plays a critical role in dynein arm assembly and motile cilia function. Mutations in this gene result in primary ciliary dyskinesia. Naturally occuring readthrough transcription occurs from this locus to the downstream t-complex 10 like (TCP10L) gene. [provided by RefSeq, Apr 2017]

CFAP298 links:

CFAP298-TCP10L (HGNC:):

CFAP298-TCP10L 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=-0.78).

BP6

Variant 21-32602012-G-A is Benign according to our data. Variant chr21-32602012-G-A is described in ClinVar as [Benign]. Clinvar id is 1248500.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP298	NM_021254.4 linkuse as main transcript	c.763-39C>T		intron_variant		ENST00000290155.8	NP_067077.1
CFAP298-TCP10L	NR_146638.2 linkuse as main transcript	n.800+1149C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP298	ENST00000290155.8 linkuse as main transcript	c.763-39C>T		intron_variant		1	NM_021254.4	ENSP00000290155	P1

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18326

AN:

152046

Hom.:

1608

Cov.:

show subpopulations

Gnomad AFR

AF:

0.248

Gnomad AMI

AF:

0.0571

Gnomad AMR

AF:

0.0705

Gnomad ASJ

AF:

0.0931

Gnomad EAS

AF:

0.0877

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.0434

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.0711

Gnomad OTH

AF:

0.103

GnomAD3 exomes

AF:

0.0853

AC:

21175

AN:

248328

Hom.:

1221

AF XY:

0.0851

AC XY:

11449

AN XY:

134524

show subpopulations

Gnomad AFR exome

AF:

0.254

Gnomad AMR exome

AF:

0.0462

Gnomad ASJ exome

AF:

0.0888

Gnomad EAS exome

AF:

0.0815

Gnomad SAS exome

AF:

0.119

Gnomad FIN exome

AF:

0.0415

Gnomad NFE exome

AF:

0.0715

Gnomad OTH exome

AF:

0.0845

GnomAD4 exome

AF:

0.0756

AC:

87403

AN:

1156378

Hom.:

4128

Cov.:

AF XY:

0.0773

AC XY:

45673

AN XY:

590622

show subpopulations

Gnomad4 AFR exome

AF:

0.249

Gnomad4 AMR exome

AF:

0.0490

Gnomad4 ASJ exome

AF:

0.0855

Gnomad4 EAS exome

AF:

0.0969

Gnomad4 SAS exome

AF:

0.118

Gnomad4 FIN exome

AF:

0.0406

Gnomad4 NFE exome

AF:

0.0665

Gnomad4 OTH exome

AF:

0.0910

GnomAD4 genome

AF:

0.121

AC:

18358

AN:

152164

Hom.:

1614

Cov.:

AF XY:

0.119

AC XY:

8860

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.248

Gnomad4 AMR

AF:

0.0705

Gnomad4 ASJ

AF:

0.0931

Gnomad4 EAS

AF:

0.0881

Gnomad4 SAS

AF:

0.116

Gnomad4 FIN

AF:

0.0434

Gnomad4 NFE

AF:

0.0711

Gnomad4 OTH

AF:

0.109

Alfa

AF:

0.0878

Hom.:

421

Bravo

AF:

0.126

Asia WGS

AF:

0.153

AC:

531

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 16, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

7.4

DANN

Benign

0.77

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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