20-20073032-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015585.4(CFAP61):c.295-1270T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 152,148 control chromosomes in the GnomAD database, including 44,583 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 0.76 (44583 hom., cov: 32)
• Consequence: CFAP61 NM_015585.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP61	NM_015585.4	c.295-1270T>C		intron_variant		ENST00000245957.10
CFAP61	NM_001167816.1	c.295-1270T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP61	ENST00000245957.10	c.295-1270T>C		intron_variant		1	NM_015585.4	P1

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115882 AN: 152030 Hom.: 44542 Cov.: 32

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.762 AC: 115981 AN: 152148 Hom.: 44583 Cov.: 32 AF XY: 0.762 AC XY: 56689 AN XY: 74390

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.743

Alfa AF: 0.724 Hom.: 51226

Bravo AF: 0.773

Asia WGS AF: 0.833 AC: 2897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.0
Dann	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs6046593; hg19: chr20-20053676;