rs6046805

chr20-20343697-G-Achr20-20343697-G-C

Variant summary

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

The NM_015585.4(CFAP61):c.3513+1776G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,990 control chromosomes in the GnomAD database, including 13,610 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 0.41 (13610 hom., cov: 32)
• Consequence: CFAP61 NM_015585.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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 = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP61	NM_015585.4	c.3513+1776G>A		intron_variant		ENST00000245957.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP61	ENST00000245957.10	c.3513+1776G>A		intron_variant		1	NM_015585.4	P1
CFAP61	ENST00000377308.6	c.*290+1776G>A		intron_variant, NMD_transcript_variant		2
CFAP61	ENST00000674445.1	n.1114+1776G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62622 AN: 151872 Hom.: 13600 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.412 AC: 62657 AN: 151990 Hom.: 13610 Cov.: 32 AF XY: 0.413 AC XY: 30716 AN XY: 74298

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.411

Alfa AF: 0.448 Hom.: 22162

Bravo AF: 0.398

Asia WGS AF: 0.505 AC: 1761 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	0.80
Dann	Benign	0.75

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: rs6046805; hg19: chr20-20324341;