chr7-23643042-C-G

Variant names:

• chr7-23643042-C-G
• rs1783391864
• NM_138771.4:c.350C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_138771.4(CCDC126):​c.350C>G​(p.Thr117Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CCDC126 NM_138771.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.20
• Publications: 0 publications found

Genes affected

CCDC126 (HGNC:22398): (coiled-coil domain containing 126) Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=0.13730353).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138771.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC126	NM_138771.4	MANE Select	c.350C>G	p.Thr117Ser	missense	Exon 4 of 4	NP_620126.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC126	ENST00000307471.8	TSL:1 MANE Select	c.350C>G	p.Thr117Ser	missense	Exon 4 of 4	ENSP00000304355.3	Q96EE4
	CCDC126	ENST00000409765.5	TSL:1	c.350C>G	p.Thr117Ser	missense	Exon 3 of 3	ENSP00000386675.1	Q96EE4
	CCDC126	ENST00000410069.1	TSL:1	c.350C>G	p.Thr117Ser	missense	Exon 4 of 4	ENSP00000386355.1	Q96EE4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.45
CADD	Benign	18
DANN	Benign	0.97
DEOGEN2	Benign	0.010	T
Eigen	Benign	0.10
Eigen_PC	Uncertain	0.31
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.67	T
M_CAP	Benign	0.0063	T
MetaRNN	Benign	0.14	T
MetaSVM	Benign	-0.89	T
MutationAssessor	Benign	1.7	L
PhyloP100		6.2
PrimateAI	Uncertain	0.51	T
PROVEAN	Benign	0.15	N
REVEL	Benign	0.077
Sift	Benign	0.30	T
Sift4G	Benign	0.55	T
Polyphen		0.0	B
Vest4		0.20
MutPred		0.17		Gain of disorder (P = 0.0831)
MVP		0.13
MPC		0.18
ClinPred		0.79	D
GERP RS		5.9
Varity_R		0.050
gMVP		0.28
Mutation Taster		=93/7	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: rs1783391864; hg19: chr7-23682661;