rs10516647

Variant names:

• chr4-80715499-A-G
• rs10516647
• NM_152770.3:c.333+132316A>G

Variant summary

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

The NM_152770.3(CFAP299):​c.333+132316A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0166 in 152,120 control chromosomes in the GnomAD database, including 52 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 0.017 (52 hom., cov: 32)
• Consequence: CFAP299 NM_152770.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.70
• Publications: 2 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP299	NM_152770.3	c.333+132316A>G		intron_variant	Intron 3 of 5	ENST00000358105.8	NP_689983.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP299	ENST00000358105.8	c.333+132316A>G		intron_variant	Intron 3 of 5	1	NM_152770.3	ENSP00000350818.3
CFAP299	ENST00000508675.1	c.384+107116A>G		intron_variant	Intron 4 of 6	1		ENSP00000425786.1
CFAP299	ENST00000502497.5	n.360-74876A>G		intron_variant	Intron 3 of 3	3
CFAP299	ENST00000513920.5	n.451+75664A>G		intron_variant	Intron 4 of 5	2		ENSP00000422569.1

Frequencies

GnomAD3 genomes AF: 0.0166 AC: 2527 AN: 152002 Hom.: 52 Cov.: 32

Gnomad AFR AF: 0.00502

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.0254

Gnomad SAS AF: 0.0424

Gnomad FIN AF: 0.00631

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0143

Gnomad OTH AF: 0.0168

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

GnomAD4 genome AF: 0.0166 AC: 2532 AN: 152120 Hom.: 52 Cov.: 32 AF XY: 0.0174 AC XY: 1295 AN XY: 74354

African (AFR) AF: 0.00508 AC: 211 AN: 41546

American (AMR) AF: 0.0577 AC: 879 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3470

East Asian (EAS) AF: 0.0253 AC: 131 AN: 5178

South Asian (SAS) AF: 0.0429 AC: 207 AN: 4826

European-Finnish (FIN) AF: 0.00631 AC: 67 AN: 10618

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0143 AC: 974 AN: 67936

Other (OTH) AF: 0.0171 AC: 36 AN: 2108

Alfa AF: 0.0164 Hom.: 2

Bravo AF: 0.0206

Asia WGS AF: 0.0360 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	15
DANN	Benign	0.67
PhyloP100		2.7
Mutation Taster		=100/0	polymorphism

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: rs10516647; hg19: chr4-81636653;