dbSNP rs2328500: CFAP61:c.*129G>A (chr20-20171937-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

6 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CFAP61	NM_015585.4 link	c.1385+2477G>A		intron_variant	Intron 13 of 26	ENST00000245957.10	NP_056400.3	Q8NHU2-1
CFAP61	NM_001167816.1 link	c.*129G>A		3_prime_UTR_variant	Exon 13 of 13		NP_001161288.1	Q8NHU2-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP61	ENST00000245957.10 link	c.1385+2477G>A		intron_variant	Intron 13 of 26	1	NM_015585.4	ENSP00000245957.5		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

African (AFR)

AF:

0.927

AC:

7650

AN:

8250

American (AMR)

AF:

0.794

AC:

7422

AN:

9342

Ashkenazi Jewish (ASJ)

AF:

0.962

AC:

10690

AN:

11112

East Asian (EAS)

AF:

0.362

AC:

8942

AN:

24726

South Asian (SAS)

AF:

0.869

AC:

18268

AN:

21016

European-Finnish (FIN)

AF:

0.890

AC:

34779

AN:

39066

Middle Eastern (MID)

AF:

0.969

AC:

3162

AN:

3264

European-Non Finnish (NFE)

AF:

0.942

AC:

192171

AN:

204092

Other (OTH)

AF:

0.901

AC:

18194

AN:

20204

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

1222

2444

3666

4888

6110

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

494

988

1482

1976

2470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.900

AC:

136775

AN:

152030

Hom.:

62344

Cov.:

AF XY:

0.892

AC XY:

66306

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.915

AC:

37933

AN:

41476

American (AMR)

AF:

0.837

AC:

12756

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.962

AC:

3339

AN:

3472

East Asian (EAS)

AF:

0.399

AC:

2047

AN:

5128

South Asian (SAS)

AF:

0.874

AC:

4203

AN:

4808

European-Finnish (FIN)

AF:

0.879

AC:

9292

AN:

10576

Middle Eastern (MID)

AF:

0.986

AC:

290

AN:

294

European-Non Finnish (NFE)

AF:

0.943

AC:

64108

AN:

68010

Other (OTH)

AF:

0.904

AC:

1912

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

607

1215

1822

2430

3037

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

890

1780

2670

3560

4450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.932

Hom.:

33801

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

(source)

DANN

Benign

0.84

PhyloP100

-0.28

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over