rs10022464

Positions:

• chr4-80672245-G-A
• chr4-80672245-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_152770.3(CFAP299):​c.333+89062G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00719 in 152,252 control chromosomes in the GnomAD database, including 4 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 0.0072 (4 hom., cov: 32)
• Consequence: CFAP299 NM_152770.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

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

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP299	NM_152770.3	c.333+89062G>A		intron_variant		ENST00000358105.8	NP_689983.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP299	ENST00000358105.8	c.333+89062G>A		intron_variant		1	NM_152770.3	ENSP00000350818	P1
CFAP299	ENST00000508675.1	c.384+63862G>A		intron_variant		1		ENSP00000425786
CFAP299	ENST00000513920.5	c.451+32410G>A		intron_variant, NMD_transcript_variant		2		ENSP00000422569
CFAP299	ENST00000502497.5	n.359+89062G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.00721 AC: 1097 AN: 152136 Hom.: 4 Cov.: 32

Gnomad AFR AF: 0.00210

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.00642

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00801

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.00335

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

GnomAD4 genome AF: 0.00719 AC: 1095 AN: 152252 Hom.: 4 Cov.: 32 AF XY: 0.00672 AC XY: 500 AN XY: 74460

Gnomad4 AFR AF: 0.00209

Gnomad4 AMR AF: 0.00641

Gnomad4 ASJ AF: 0.00375

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00801

Gnomad4 NFE AF: 0.0118

Gnomad4 OTH AF: 0.00332

Alfa AF: 0.00905 Hom.: 0

Bravo AF: 0.00673

Asia WGS AF: 0.00173 AC: 6 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	2.6
DANN	Benign	0.52

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: rs10022464; hg19: chr4-81593399;