Variant chr1-1955672-GC-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001304360.2(CFAP74):c.2176+18del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 1,612,216 control chromosomes in the GnomAD database, including 54,719 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.22 ( 4067 hom., cov: 28)

Exomes 𝑓: 0.26 ( 50652 hom. )

Consequence

CFAP74
NM_001304360.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0880

Variant links:

Genes affected

CFAP74 (HGNC:29368): (cilia and flagella associated protein 74) Predicted to be involved in axoneme assembly. Predicted to be located in axoneme. [provided by Alliance of Genome Resources, Apr 2022]

CFAP74 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP74	NM_001304360.2 linkuse as main transcript	c.2176+18del		intron_variant		ENST00000682832.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP74	ENST00000682832.2 linkuse as main transcript	c.2176+18del		intron_variant			NM_001304360.2	P2

Frequencies

GnomAD3 genomes

AF:

0.220

AC:

33381

AN:

151792

Hom.:

4068

Cov.:

show subpopulations

Gnomad AFR

AF:

0.141

Gnomad AMI

AF:

0.274

Gnomad AMR

AF:

0.217

Gnomad ASJ

AF:

0.254

Gnomad EAS

AF:

0.210

Gnomad SAS

AF:

0.180

Gnomad FIN

AF:

0.225

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.222

GnomAD3 exomes

AF:

0.184

AC:

39879

AN:

216886

Hom.:

6282

AF XY:

0.187

AC XY:

22143

AN XY:

118166

show subpopulations

Gnomad AFR exome

AF:

0.0848

Gnomad AMR exome

AF:

0.176

Gnomad ASJ exome

AF:

0.224

Gnomad EAS exome

AF:

0.128

Gnomad SAS exome

AF:

0.143

Gnomad FIN exome

AF:

0.182

Gnomad NFE exome

AF:

0.217

Gnomad OTH exome

AF:

0.191

GnomAD4 exome

AF:

0.260

AC:

379999

AN:

1460304

Hom.:

50652

Cov.:

AF XY:

0.259

AC XY:

188265

AN XY:

726472

show subpopulations

Gnomad4 AFR exome

AF:

0.137

Gnomad4 AMR exome

AF:

0.236

Gnomad4 ASJ exome

AF:

0.257

Gnomad4 EAS exome

AF:

0.260

Gnomad4 SAS exome

AF:

0.190

Gnomad4 FIN exome

AF:

0.225

Gnomad4 NFE exome

AF:

0.273

Gnomad4 OTH exome

AF:

0.248

GnomAD4 genome

AF:

0.220

AC:

33376

AN:

151912

Hom.:

4067

Cov.:

AF XY:

0.216

AC XY:

16024

AN XY:

74236

show subpopulations

Gnomad4 AFR

AF:

0.140

Gnomad4 AMR

AF:

0.217

Gnomad4 ASJ

AF:

0.254

Gnomad4 EAS

AF:

0.210

Gnomad4 SAS

AF:

0.182

Gnomad4 FIN

AF:

0.225

Gnomad4 NFE

AF:

0.269

Gnomad4 OTH

AF:

0.219

Alfa

AF:

0.130

Hom.:

438

Asia WGS

AF:

0.183

AC:

638

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over