rs10516646

Positions:

• chr4-80684634-G-A
• chr4-80684634-G-C

Variant summary

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

The NM_152770.3(CFAP299):​c.333+101451G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0966 in 152,148 control chromosomes in the GnomAD database, including 1,066 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 0.097 (1066 hom., cov: 31)
• Consequence: CFAP299 NM_152770.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP299	NM_152770.3	c.333+101451G>A		intron_variant		ENST00000358105.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP299	ENST00000358105.8	c.333+101451G>A		intron_variant		1	NM_152770.3	P1
CFAP299	ENST00000508675.1	c.384+76251G>A		intron_variant		1
CFAP299	ENST00000513920.5	c.451+44799G>A		intron_variant, NMD_transcript_variant		2
CFAP299	ENST00000502497.5	n.359+101451G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0964 AC: 14656 AN: 152030 Hom.: 1059 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0639

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0472

Gnomad OTH AF: 0.0884

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

GnomAD4 genome AF: 0.0966 AC: 14693 AN: 152148 Hom.: 1066 Cov.: 31 AF XY: 0.0990 AC XY: 7365 AN XY: 74378

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.0639

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.0475

Gnomad4 NFE AF: 0.0471

Gnomad4 OTH AF: 0.0861

Alfa AF: 0.0554 Hom.: 214

Bravo AF: 0.101

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	0.77

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: rs10516646; hg19: chr4-81605788;