chr4-80463695-C-T

Variant names:

• chr4-80463695-C-T
• rs9942234
• NM_152770.3:c.242+100811C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152770.3(CFAP299):​c.242+100811C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0726 in 152,076 control chromosomes in the GnomAD database, including 1,302 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 0.073 (1302 hom., cov: 32)
• Consequence: CFAP299 NM_152770.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848
• Publications: 0 publications found

Genes affected

CFAP299 (HGNC:28554): (cilia and flagella associated protein 299) Predicted to be located in cytoplasm. [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 (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152770.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP299	NM_152770.3	MANE Select	c.242+100811C>T		intron	N/A	NP_689983.2
	CFAP299	NM_001206997.2		c.242+100811C>T		intron	N/A	NP_001193926.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP299	ENST00000358105.8	TSL:1 MANE Select	c.242+100811C>T		intron	N/A	ENSP00000350818.3
	CFAP299	ENST00000508675.1	TSL:1	c.242+100811C>T		intron	N/A	ENSP00000425786.1
	CFAP299	ENST00000502497.5	TSL:3	n.268+100811C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0723 AC: 10993 AN: 151958 Hom.: 1295 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0321

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.00946

Gnomad SAS AF: 0.0184

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00116

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0726 AC: 11038 AN: 152076 Hom.: 1302 Cov.: 32 AF XY: 0.0705 AC XY: 5245 AN XY: 74348

African (AFR) AF: 0.247 AC: 10215 AN: 41428

American (AMR) AF: 0.0320 AC: 489 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.00259 AC: 9 AN: 3470

East Asian (EAS) AF: 0.00909 AC: 47 AN: 5168

South Asian (SAS) AF: 0.0185 AC: 89 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10602

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00116 AC: 79 AN: 68008

Other (OTH) AF: 0.0507 AC: 107 AN: 2112

Alfa AF: 0.0323 Hom.: 190

Bravo AF: 0.0842

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.69
DANN	Benign	0.58
PhyloP100		-0.85
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: rs9942234; hg19: chr4-81384849;