20-20082346-T-C

Variant names:

• chr20-20082346-T-C
• rs6046605
• NM_015585.4:c.566+6731T>C

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+6731T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,136 control chromosomes in the GnomAD database, including 34,087 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 0.67 (34087 hom., cov: 33)
• Consequence: CFAP61 NM_015585.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• 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]

ENSG00000300020 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 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+6731T>C		intron	N/A	NP_056400.3
	CFAP61	NM_001167816.1		c.566+6731T>C		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+6731T>C		intron	N/A	ENSP00000245957.5	Q8NHU2-1
	CFAP61	ENST00000451767.6	TSL:1	c.566+6731T>C		intron	N/A	ENSP00000414537.2	Q8NHU2-3
	CFAP61	ENST00000340348.10	TSL:1	c.428+6731T>C		intron	N/A	ENSP00000345553.6	F8W6E2

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101293 AN: 152016 Hom.: 34030 Cov.: 33

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.667 AC: 101411 AN: 152136 Hom.: 34087 Cov.: 33 AF XY: 0.666 AC XY: 49560 AN XY: 74368

African (AFR) AF: 0.724 AC: 30073 AN: 41522

American (AMR) AF: 0.696 AC: 10641 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2219 AN: 3472

East Asian (EAS) AF: 0.824 AC: 4258 AN: 5168

South Asian (SAS) AF: 0.726 AC: 3502 AN: 4824

European-Finnish (FIN) AF: 0.634 AC: 6696 AN: 10566

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41662 AN: 67974

Other (OTH) AF: 0.660 AC: 1393 AN: 2110

Alfa AF: 0.636 Hom.: 90967

Bravo AF: 0.675

Asia WGS AF: 0.747 AC: 2599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.079
DANN	Benign	0.68
PhyloP100		-2.0
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: rs6046605; hg19: chr20-20062990;