rs2424295

Variant names:

• chr20-20236683-T-G
• rs2424295
• NM_015585.4:c.2060+8307T>G

Variant summary

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

The NM_015585.4(CFAP61):​c.2060+8307T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,274 control chromosomes in the GnomAD database, including 896 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 0.10 (896 hom., cov: 32)
• Consequence: CFAP61 NM_015585.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.901
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.124 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.2060+8307T>G		intron	N/A	NP_056400.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP61	ENST00000245957.10	TSL:1 MANE Select	c.2060+8307T>G		intron	N/A	ENSP00000245957.5
	CFAP61	ENST00000377293.5	TSL:1	c.128+8307T>G		intron	N/A	ENSP00000366508.1
	CFAP61	ENST00000389656.4	TSL:1	c.128+8307T>G		intron	N/A	ENSP00000374307.3

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15910 AN: 152156 Hom.: 897 Cov.: 32

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0890

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0221

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.104 AC: 15910 AN: 152274 Hom.: 896 Cov.: 32 AF XY: 0.107 AC XY: 7998 AN XY: 74442

African (AFR) AF: 0.0746 AC: 3099 AN: 41558

American (AMR) AF: 0.0889 AC: 1361 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3470

East Asian (EAS) AF: 0.0220 AC: 114 AN: 5188

South Asian (SAS) AF: 0.132 AC: 638 AN: 4828

European-Finnish (FIN) AF: 0.162 AC: 1720 AN: 10588

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8136 AN: 68018

Other (OTH) AF: 0.115 AC: 244 AN: 2116

Alfa AF: 0.117 Hom.: 699

Bravo AF: 0.0950

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.3
DANN	Benign	0.57
PhyloP100		0.90
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: rs2424295; hg19: chr20-20217327;