4-80868416-C-T

Variant names:

• chr4-80868416-C-T
• rs1493182
• NM_152770.3:c.334-1577C>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.334-1577C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,014 control chromosomes in the GnomAD database, including 14,490 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 0.36 (14490 hom., cov: 32)
• Consequence: CFAP299 NM_152770.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.630
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP299	NM_152770.3	c.334-1577C>T		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.334-1577C>T		intron_variant	Intron 3 of 5	1	NM_152770.3	ENSP00000350818.3
CFAP299	ENST00000508675.1	c.385-1577C>T		intron_variant	Intron 4 of 6	1		ENSP00000425786.1
CFAP299	ENST00000513920.5	n.452-1577C>T		intron_variant	Intron 4 of 5	2		ENSP00000422569.1

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54617 AN: 151896 Hom.: 14460 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.360 AC: 54704 AN: 152014 Hom.: 14490 Cov.: 32 AF XY: 0.356 AC XY: 26450 AN XY: 74320

African (AFR) AF: 0.747 AC: 30945 AN: 41428

American (AMR) AF: 0.254 AC: 3884 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1180 AN: 3464

East Asian (EAS) AF: 0.284 AC: 1468 AN: 5176

South Asian (SAS) AF: 0.386 AC: 1859 AN: 4818

European-Finnish (FIN) AF: 0.159 AC: 1682 AN: 10572

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12621 AN: 67962

Other (OTH) AF: 0.332 AC: 702 AN: 2114

Alfa AF: 0.228 Hom.: 7273

Bravo AF: 0.384

Asia WGS AF: 0.388 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.9
DANN	Benign	0.57
PhyloP100		0.63
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: rs1493182; hg19: chr4-81789570;