20-20073032-T-C

Variant names:

• chr20-20073032-T-C
• rs6046593
• NM_015585.4:c.295-1270T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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]

ENSG00000309008 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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.295-1270T>C		intron	N/A	NP_056400.3
	CFAP61	NM_001167816.1		c.295-1270T>C		intron	N/A	NP_001161288.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP61	ENST00000245957.10	TSL:1 MANE Select	c.295-1270T>C		intron	N/A	ENSP00000245957.5
	CFAP61	ENST00000451767.6	TSL:1	c.295-1270T>C		intron	N/A	ENSP00000414537.2
	CFAP61	ENST00000340348.10	TSL:1	c.157-1270T>C		intron	N/A	ENSP00000345553.6

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

African (AFR) AF: 0.840 AC: 34873 AN: 41520

American (AMR) AF: 0.771 AC: 11791 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2524 AN: 3472

East Asian (EAS) AF: 0.918 AC: 4752 AN: 5178

South Asian (SAS) AF: 0.832 AC: 4017 AN: 4830

European-Finnish (FIN) AF: 0.700 AC: 7396 AN: 10566

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48092 AN: 67976

Other (OTH) AF: 0.743 AC: 1567 AN: 2110

Alfa AF: 0.728 Hom.: 66007

Bravo AF: 0.773

Asia WGS AF: 0.833 AC: 2897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.74
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6046593; hg19: chr20-20053676;