20-20058862-T-A

Variant names:

• chr20-20058862-T-A
• rs6035539
• NM_015585.4:c.143+2066T>A

Variant summary

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

The NM_015585.4(CFAP61):​c.143+2066T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,052 control chromosomes in the GnomAD database, including 30,209 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 0.63 (30209 hom., cov: 32)
• Consequence: CFAP61 NM_015585.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP61	NM_015585.4	MANE Select	c.143+2066T>A		intron	N/A	NP_056400.3
	CFAP61	NM_001167816.1		c.143+2066T>A		intron	N/A	NP_001161288.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP61	ENST00000245957.10	TSL:1 MANE Select	c.143+2066T>A		intron	N/A	ENSP00000245957.5
	CFAP61	ENST00000451767.6	TSL:1	c.143+2066T>A		intron	N/A	ENSP00000414537.2
	CFAP61	ENST00000340348.10	TSL:1	c.5+6271T>A		intron	N/A	ENSP00000345553.6

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95139 AN: 151934 Hom.: 30166 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.626 AC: 95245 AN: 152052 Hom.: 30209 Cov.: 32 AF XY: 0.629 AC XY: 46779 AN XY: 74346

African (AFR) AF: 0.620 AC: 25679 AN: 41430

American (AMR) AF: 0.702 AC: 10725 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2014 AN: 3472

East Asian (EAS) AF: 0.937 AC: 4862 AN: 5190

South Asian (SAS) AF: 0.641 AC: 3094 AN: 4826

European-Finnish (FIN) AF: 0.650 AC: 6872 AN: 10578

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.587 AC: 39883 AN: 67964

Other (OTH) AF: 0.608 AC: 1280 AN: 2106

Alfa AF: 0.594 Hom.: 3371

Bravo AF: 0.634

Asia WGS AF: 0.748 AC: 2599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.38
PhyloP100		-1.3
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: rs6035539; hg19: chr20-20039506;