rs3213706

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001195637.2(CCDC179):​c.86G>T​(p.Arg29Leu) variant causes a missense 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. 11/16 in silico tools predict 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)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

CCDC179
NM_001195637.2 missense

Scores

2
1
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01
Variant links:
Genes affected
CCDC179 (HGNC:44653): (coiled-coil domain containing 179)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.24647051).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CCDC179NM_001195637.2 linkuse as main transcriptc.86G>T p.Arg29Leu missense_variant 2/4 ENST00000532798.3 NP_001182566.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CCDC179ENST00000532798.3 linkuse as main transcriptc.86G>T p.Arg29Leu missense_variant 2/42 NM_001195637.2 ENSP00000457511 P1
ENST00000499625.1 linkuse as main transcriptn.484+21092C>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1336046
Hom.:
0
Cov.:
28
AF XY:
0.00
AC XY:
0
AN XY:
657686
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.17
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.40
CADD
Benign
6.6
DANN
Benign
0.71
DEOGEN2
Benign
0.065
T
FATHMM_MKL
Benign
0.018
N
LIST_S2
Benign
0.50
T
M_CAP
Benign
0.0094
T
MetaRNN
Benign
0.25
T
MutationTaster
Benign
1.0
P
PrimateAI
Benign
0.33
T
PROVEAN
Pathogenic
-6.0
D
Sift
Uncertain
0.027
D
Sift4G
Pathogenic
0.0
D
Vest4
0.41
MVP
0.36
GERP RS
-3.0
Varity_R
0.11
gMVP
0.050

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: rs3213706; hg19: chr11-22881002; API