chr20-20171937-G-A

Variant names:

• chr20-20171937-G-A
• rs2328500
• ENST00000451767.6:c.*129G>A

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.84).
• 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 rank	MANE	Protein	UniProt
CFAP61	NM_015585.4	c.1385+2477G>A		intron_variant	Intron 13 of 26	ENST00000245957.10	NP_056400.3
CFAP61	NM_001167816.1	c.*129G>A		3_prime_UTR_variant	Exon 13 of 13		NP_001161288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP61	ENST00000245957.10	c.1385+2477G>A		intron_variant	Intron 13 of 26	1	NM_015585.4	ENSP00000245957.5

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

African (AFR) AF: 0.927 AC: 7650 AN: 8250

American (AMR) AF: 0.794 AC: 7422 AN: 9342

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 10690 AN: 11112

East Asian (EAS) AF: 0.362 AC: 8942 AN: 24726

South Asian (SAS) AF: 0.869 AC: 18268 AN: 21016

European-Finnish (FIN) AF: 0.890 AC: 34779 AN: 39066

Middle Eastern (MID) AF: 0.969 AC: 3162 AN: 3264

European-Non Finnish (NFE) AF: 0.942 AC: 192171 AN: 204092

Other (OTH) AF: 0.901 AC: 18194 AN: 20204

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

African (AFR) AF: 0.915 AC: 37933 AN: 41476

American (AMR) AF: 0.837 AC: 12756 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 3339 AN: 3472

East Asian (EAS) AF: 0.399 AC: 2047 AN: 5128

South Asian (SAS) AF: 0.874 AC: 4203 AN: 4808

European-Finnish (FIN) AF: 0.879 AC: 9292 AN: 10576

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.943 AC: 64108 AN: 68010

Other (OTH) AF: 0.904 AC: 1912 AN: 2114

Alfa AF: 0.932 Hom.: 33801

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
PhyloP100		-0.28
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: rs2328500; hg19: chr20-20152581; COSMIC: COSV55637717;