rs2424295

Positions:

• chr20-20236683-T-G

Variant summary

Our verdict is Benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP61	NM_015585.4	c.2060+8307T>G		intron_variant		ENST00000245957.10	NP_056400.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP61	ENST00000245957.10	c.2060+8307T>G		intron_variant		1	NM_015585.4	ENSP00000245957.5

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

Gnomad4 AFR AF: 0.0746

Gnomad4 AMR AF: 0.0889

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.0220

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.115

Alfa AF: 0.117 Hom.: 637

Bravo AF: 0.0950

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.3
DANN	Benign	0.57

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

LitVar

Other links and lift over

dbSNP: rs2424295; hg19: chr20-20217327;