20-20105886-A-G

Position:

• chr20-20105886-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP61	NM_015585.4	c.859+7072A>G		intron_variant		ENST00000245957.10	NP_056400.3
CFAP61	NM_001167816.1	c.859+7072A>G		intron_variant			NP_001161288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP61	ENST00000245957.10	c.859+7072A>G		intron_variant		1	NM_015585.4	ENSP00000245957	P1

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

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.844

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.804

Alfa AF: 0.748 Hom.: 4943

Bravo AF: 0.801

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.15

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