20-20082346-T-C

Position:

• chr20-20082346-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.566+6731T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,136 control chromosomes in the GnomAD database, including 34,087 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 0.67 (34087 hom., cov: 33)
• Consequence: CFAP61 NM_015585.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP61	NM_015585.4	c.566+6731T>C		intron_variant		ENST00000245957.10	NP_056400.3
CFAP61	NM_001167816.1	c.566+6731T>C		intron_variant			NP_001161288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP61	ENST00000245957.10	c.566+6731T>C		intron_variant		1	NM_015585.4	ENSP00000245957.5

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101293 AN: 152016 Hom.: 34030 Cov.: 33

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.667 AC: 101411 AN: 152136 Hom.: 34087 Cov.: 33 AF XY: 0.666 AC XY: 49560 AN XY: 74368

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.824

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.660

Alfa AF: 0.627 Hom.: 52113

Bravo AF: 0.675

Asia WGS AF: 0.747 AC: 2599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.079
DANN	Benign	0.68

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: rs6046605; hg19: chr20-20062990;