Variant rs2328500 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000451767.6(CFAP61):c.*129G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 493,102 control chromosomes in the GnomAD database, including 199,466 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.90 ( 62344 hom., cov: 29)

Exomes 𝑓: 0.88 ( 137122 hom. )

Consequence

CFAP61
ENST00000451767.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.285

Variant links:

Genes affected

CFAP61 (HGNC:15872): (cilia and flagella associated protein 61) Predicted to be involved in cilium movement and cilium organization. Predicted to be located in axoneme and motile cilium. Predicted to colocalize with radial spoke stalk. [provided by Alliance of Genome Resources, Apr 2022]

CFAP61 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP61	NM_015585.4 linkuse as main transcript	c.1385+2477G>A		intron_variant		ENST00000245957.10	NP_056400.3
CFAP61	NM_001167816.1 linkuse as main transcript	c.*129G>A		3_prime_UTR_variant	13/13		NP_001161288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP61	ENST00000245957.10 linkuse as main transcript	c.1385+2477G>A		intron_variant		1	NM_015585.4	ENSP00000245957	P1	Q8NHU2-1

Frequencies

GnomAD3 genomes

AF:

0.900

AC:

136691

AN:

151912

Hom.:

62311

Cov.:

show subpopulations

Gnomad AFR

AF:

0.915

Gnomad AMI

AF:

0.981

Gnomad AMR

AF:

0.838

Gnomad ASJ

AF:

0.962

Gnomad EAS

AF:

0.400

Gnomad SAS

AF:

0.874

Gnomad FIN

AF:

0.879

Gnomad MID

AF:

0.987

Gnomad NFE

AF:

0.943

Gnomad OTH

AF:

0.909

GnomAD4 exome

AF:

0.883

AC:

301278

AN:

341072

Hom.:

137122

Cov.:

AF XY:

0.885

AC XY:

157797

AN XY:

178354

show subpopulations

Gnomad4 AFR exome

AF:

0.927

Gnomad4 AMR exome

AF:

0.794

Gnomad4 ASJ exome

AF:

0.962

Gnomad4 EAS exome

AF:

0.362

Gnomad4 SAS exome

AF:

0.869

Gnomad4 FIN exome

AF:

0.890

Gnomad4 NFE exome

AF:

0.942

Gnomad4 OTH exome

AF:

0.901

GnomAD4 genome

AF:

0.900

AC:

136775

AN:

152030

Hom.:

62344

Cov.:

AF XY:

0.892

AC XY:

66306

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.915

Gnomad4 AMR

AF:

0.837

Gnomad4 ASJ

AF:

0.962

Gnomad4 EAS

AF:

0.399

Gnomad4 SAS

AF:

0.874

Gnomad4 FIN

AF:

0.879

Gnomad4 NFE

AF:

0.943

Gnomad4 OTH

AF:

0.904

Alfa

AF:

0.931

Hom.:

30074

Bravo

AF:

0.894

Asia WGS

AF:

0.690

AC:

2402

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.5

DANN

Benign

0.84

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