chr20-20105886-A-G

Variant names:

• chr20-20105886-A-G
• rs6046627
• NM_015585.4:c.859+7072A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015585.4(CFAP61):​c.859+7072A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 148,590 control chromosomes in the GnomAD database, including 46,873 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 0.79 (46873 hom., cov: 25)
• Consequence: CFAP61 NM_015585.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP61	NM_015585.4	MANE Select	c.859+7072A>G		intron	N/A	NP_056400.3
	CFAP61	NM_001167816.1		c.859+7072A>G		intron	N/A	NP_001161288.1	Q8NHU2-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP61	ENST00000245957.10	TSL:1 MANE Select	c.859+7072A>G		intron	N/A	ENSP00000245957.5	Q8NHU2-1
	CFAP61	ENST00000451767.6	TSL:1	c.859+7072A>G		intron	N/A	ENSP00000414537.2	Q8NHU2-3
	CFAP61	ENST00000340348.10	TSL:1	c.721+7072A>G		intron	N/A	ENSP00000345553.6	F8W6E2

Frequencies

GnomAD3 genomes AF: 0.792 AC: 117539 AN: 148500 Hom.: 46832 Cov.: 25

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.795

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.792 AC: 117628 AN: 148590 Hom.: 46873 Cov.: 25 AF XY: 0.793 AC XY: 57439 AN XY: 72402

African (AFR) AF: 0.841 AC: 34191 AN: 40652

American (AMR) AF: 0.844 AC: 12652 AN: 14996

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2602 AN: 3440

East Asian (EAS) AF: 0.988 AC: 4900 AN: 4958

South Asian (SAS) AF: 0.869 AC: 4094 AN: 4712

European-Finnish (FIN) AF: 0.747 AC: 7022 AN: 9404

Middle Eastern (MID) AF: 0.788 AC: 227 AN: 288

European-Non Finnish (NFE) AF: 0.737 AC: 49520 AN: 67198

Other (OTH) AF: 0.804 AC: 1638 AN: 2038

Alfa AF: 0.748 Hom.: 4943

Bravo AF: 0.801

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.15
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6046627; hg19: chr20-20086530; COSMIC: COSV55650201;