20-20079071-C-T

Position:

• chr20-20079071-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP61	NM_015585.4	c.566+3456C>T		intron_variant		ENST00000245957.10
CFAP61	NM_001167816.1	c.566+3456C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP61	ENST00000245957.10	c.566+3456C>T		intron_variant		1	NM_015585.4	P1

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

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.198

Alfa AF: 0.212 Hom.: 2182

Bravo AF: 0.213

Asia WGS AF: 0.426 AC: 1478 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.37

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: rs9808594; hg19: chr20-20059715;