rs1680785

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001394090.1(CFAP92):​c.2751+6727G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

CFAP92
NM_001394090.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.719
Variant links:
Genes affected
CFAP92 (HGNC:29231): (cilia and flagella associated protein 92 (putative))

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CFAP92NM_001394090.1 linkuse as main transcriptc.2751+6727G>T intron_variant ENST00000645291.3 NP_001381019.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CFAP92ENST00000645291.3 linkuse as main transcriptc.2751+6727G>T intron_variant NM_001394090.1 ENSP00000496592.2 A0A2R8YFM9
CFAP92ENST00000511438.5 linkuse as main transcriptc.1169-15640G>T intron_variant 2 ENSP00000426217.1 D6RH05
CFAP92ENST00000669741.1 linkuse as main transcriptc.561+6727G>T intron_variant ENSP00000499631.1 A0A590UJZ5
CFAP92ENST00000637488.2 linkuse as main transcriptc.330+6727G>T intron_variant 5 ENSP00000490565.2 A0A1B0GVL5

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.7
DANN
Benign
0.36

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1680785; hg19: chr3-128644816; API