chr20-20343697-G-A

Variant names:

• chr20-20343697-G-A
• rs6046805
• NM_015585.4:c.3513+1776G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-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 rank	MANE	Protein	UniProt
CFAP61	NM_015585.4	c.3513+1776G>A		intron_variant	Intron 26 of 26	ENST00000245957.10	NP_056400.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP61	ENST00000245957.10	c.3513+1776G>A		intron_variant	Intron 26 of 26	1	NM_015585.4	ENSP00000245957.5
CFAP61	ENST00000377308.6	n.*290+1776G>A		intron_variant	Intron 9 of 9	2		ENSP00000366523.2
CFAP61	ENST00000674445.1	n.1114+1776G>A		intron_variant	Intron 5 of 5

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

African (AFR) AF: 0.268 AC: 11104 AN: 41440

American (AMR) AF: 0.411 AC: 6268 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1379 AN: 3466

East Asian (EAS) AF: 0.560 AC: 2897 AN: 5170

South Asian (SAS) AF: 0.500 AC: 2409 AN: 4818

European-Finnish (FIN) AF: 0.476 AC: 5025 AN: 10554

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32346 AN: 67958

Other (OTH) AF: 0.411 AC: 867 AN: 2112

Alfa AF: 0.446 Hom.: 33062

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
PhyloP100		-1.1
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: rs6046805; hg19: chr20-20324341;