rs3213706

chr11-22859456-C-Achr11-22859456-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. 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. In-silico tool predicts a benign outcome for this variant. 10/15 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

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.24647051).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC179	NM_001195637.2	c.86G>T	p.Arg29Leu	missense_variant	2/4	ENST00000532798.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC179	ENST00000532798.3	c.86G>T	p.Arg29Leu	missense_variant	2/4	2	NM_001195637.2	P1
	ENST00000499625.1	n.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

Other links and lift over

dbSNP: rs3213706; hg19: chr11-22881002;