rs201145645

Variant names:

• chr11-99845151-A-G
• rs201145645
• NM_014361.4:c.466A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-99845151-A-G
• chr11-99845151-A-T

Variant summary

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

The NM_014361.4(CNTN5):​c.466A>G​(p.Thr156Ala) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 14/22 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. T156S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CNTN5 NM_014361.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.67
• Publications: 0 publications found

Genes affected

CNTN5 (HGNC:2175): (contactin 5) The protein encoded by this gene is a member of the immunoglobulin superfamily, and contactin family, which mediate cell surface interactions during nervous system development. This protein is a glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein that functions as a cell adhesion molecule. It may play a role in the formation of axon connections in the developing nervous system. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.466A>G	p.Thr156Ala	missense_variant	Exon 6 of 25	ENST00000524871.6	NP_055176.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN5	ENST00000524871.6	c.466A>G	p.Thr156Ala	missense_variant	Exon 6 of 25	1	NM_014361.4	ENSP00000435637.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000329 Hom.: 0

Bravo AF: 0.0000151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.045	T
BayesDel_noAF	Benign	-0.30
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.15	.;T;T;.;T;.
Eigen	Benign	-0.12
Eigen_PC	Benign	0.041
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.67	T;.;T;T;T;T
M_CAP	Benign	0.020	T
MetaRNN	Uncertain	0.45	T;T;T;T;T;T
MetaSVM	Benign	-0.85	T
MutationAssessor	Benign	1.4	L;L;L;.;.;.
PhyloP100		4.7
PrimateAI	Benign	0.33	T
PROVEAN	Benign	-1.4	N;N;N;N;N;.
REVEL	Benign	0.13
Sift	Uncertain	0.0030	D;D;D;D;T;.
Sift4G	Uncertain	0.033	D;D;D;D;D;D
Polyphen		0.0040, 0.0010	.;B;B;B;.;.
Vest4		0.18
MutPred		0.70		Gain of catalytic residue at T156 (P = 0.1351);Gain of catalytic residue at T156 (P = 0.1351);Gain of catalytic residue at T156 (P = 0.1351);.;.;.;
MVP		0.77
MPC		0.035
ClinPred		0.83	D
GERP RS		4.3
Varity_R		0.15
gMVP		0.43
Mutation Taster		=88/12	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: rs201145645; hg19: chr11-99715883;