20-20079071-C-T

Variant names:

• chr20-20079071-C-T
• rs9808594
• NM_015585.4:c.566+3456C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015585.4(CFAP61):​c.566+3456C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,110 control chromosomes in the GnomAD database, including 4,107 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 0.21 (4107 hom., cov: 32)
• Consequence: CFAP61 NM_015585.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015585.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP61	NM_015585.4	MANE Select	c.566+3456C>T		intron	N/A	NP_056400.3
	CFAP61	NM_001167816.1		c.566+3456C>T		intron	N/A	NP_001161288.1	Q8NHU2-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP61	ENST00000245957.10	TSL:1 MANE Select	c.566+3456C>T		intron	N/A	ENSP00000245957.5	Q8NHU2-1
	CFAP61	ENST00000451767.6	TSL:1	c.566+3456C>T		intron	N/A	ENSP00000414537.2	Q8NHU2-3
	CFAP61	ENST00000340348.10	TSL:1	c.428+3456C>T		intron	N/A	ENSP00000345553.6	F8W6E2

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31796 AN: 151992 Hom.: 4094 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.195

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.209 AC: 31832 AN: 152110 Hom.: 4107 Cov.: 32 AF XY: 0.214 AC XY: 15894 AN XY: 74366

African (AFR) AF: 0.118 AC: 4906 AN: 41498

American (AMR) AF: 0.278 AC: 4255 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3470

East Asian (EAS) AF: 0.652 AC: 3368 AN: 5162

South Asian (SAS) AF: 0.289 AC: 1393 AN: 4818

European-Finnish (FIN) AF: 0.193 AC: 2043 AN: 10578

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14569 AN: 67980

Other (OTH) AF: 0.198 AC: 418 AN: 2108

Alfa AF: 0.218 Hom.: 3349

Bravo AF: 0.213

Asia WGS AF: 0.426 AC: 1478 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.37
PhyloP100		-0.091
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9808594; hg19: chr20-20059715;