NM_001195637.2:c.86G>T

Variant names:

• chr11-22859456-C-A
• rs3213706
• NM_001195637.2:c.86G>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R29W) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CCDC179 NM_001195637.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 18 publications found

Genes affected

CCDC179 (HGNC:44653): (coiled-coil domain containing 179)

ENSG00000246225 (HGNC:):

LINC02718 (HGNC:54235): (long intergenic non-protein coding RNA 2718)

ACMG classification

Our verdict: Uncertain_significance. The variant received 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 rank	MANE	Protein	UniProt
CCDC179	NM_001195637.2	c.86G>T	p.Arg29Leu	missense_variant	Exon 2 of 4	ENST00000532798.3	NP_001182566.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC179	ENST00000532798.3	c.86G>T	p.Arg29Leu	missense_variant	Exon 2 of 4	2	NM_001195637.2	ENSP00000457511.1

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

African (AFR) AF: 0.00 AC: 0 AN: 30794

American (AMR) AF: 0.00 AC: 0 AN: 33316

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24012

East Asian (EAS) AF: 0.00 AC: 0 AN: 34452

South Asian (SAS) AF: 0.00 AC: 0 AN: 68254

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32110

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5408

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1052144

Other (OTH) AF: 0.00 AC: 0 AN: 55556

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
PhyloP100		-1.0
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
Mutation Taster		=98/2	polymorphism

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: rs3213706; hg19: chr11-22881002;