chr4-80614239-G-A

Variant names:

• chr4-80614239-G-A
• rs1385890
• NM_152770.3:c.333+31056G>A

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+31056G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,028 control chromosomes in the GnomAD database, including 33,758 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 0.62 (33758 hom., cov: 33)
• Consequence: CFAP299 NM_152770.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 8 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP299	NM_152770.3	c.333+31056G>A		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+31056G>A		intron_variant	Intron 3 of 5	1	NM_152770.3	ENSP00000350818.3

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94881 AN: 151910 Hom.: 33742 Cov.: 33

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.624 AC: 94925 AN: 152028 Hom.: 33758 Cov.: 33 AF XY: 0.628 AC XY: 46665 AN XY: 74320

African (AFR) AF: 0.263 AC: 10887 AN: 41390

American (AMR) AF: 0.752 AC: 11486 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2256 AN: 3470

East Asian (EAS) AF: 0.623 AC: 3224 AN: 5176

South Asian (SAS) AF: 0.570 AC: 2745 AN: 4816

European-Finnish (FIN) AF: 0.820 AC: 8678 AN: 10584

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53415 AN: 68002

Other (OTH) AF: 0.634 AC: 1337 AN: 2110

Alfa AF: 0.719 Hom.: 112298

Bravo AF: 0.604

Asia WGS AF: 0.570 AC: 1987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.46
PhyloP100		0.071
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: rs1385890; hg19: chr4-81535393;