rs2328500

chr20-20171937-G-Achr20-20171937-G-T

Variant summary

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

The ENST00000451767.6(CFAP61):c.*129G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 493,102 control chromosomes in the GnomAD database, including 199,466 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 0.90 (62344 hom., cov: 29)
  • Exomes 𝑓: 0.88 (137122 hom.)
• Consequence: CFAP61 ENST00000451767.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP61	NM_015585.4	c.1385+2477G>A		intron_variant		ENST00000245957.10
CFAP61	NM_001167816.1	c.*129G>A		3_prime_UTR_variant	13/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP61	ENST00000245957.10	c.1385+2477G>A		intron_variant		1	NM_015585.4	P1

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136691 AN: 151912 Hom.: 62311 Cov.: 29

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.909

GnomAD4 exome AF: 0.883 AC: 301278 AN: 341072 Hom.: 137122 Cov.: 2 AF XY: 0.885 AC XY: 157797 AN XY: 178354

Gnomad4 AFR exome AF: 0.927

Gnomad4 AMR exome AF: 0.794

Gnomad4 ASJ exome AF: 0.962

Gnomad4 EAS exome AF: 0.362

Gnomad4 SAS exome AF: 0.869

Gnomad4 FIN exome AF: 0.890

Gnomad4 NFE exome AF: 0.942

Gnomad4 OTH exome AF: 0.901

GnomAD4 genome AF: 0.900 AC: 136775 AN: 152030 Hom.: 62344 Cov.: 29 AF XY: 0.892 AC XY: 66306 AN XY: 74310

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.962

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.879

Gnomad4 NFE AF: 0.943

Gnomad4 OTH AF: 0.904

Alfa AF: 0.931 Hom.: 30074

Bravo AF: 0.894

Asia WGS AF: 0.690 AC: 2402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.5
Dann	Benign	0.84

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: rs2328500; hg19: chr20-20152581; COSMIC: COSV55637717;