NM_014361.4:c.55+39202C>G

Variant names:

• chr11-99595471-C-G
• rs10501918
• NM_014361.4:c.55+39202C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014361.4(CNTN5):​c.55+39202C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 151,870 control chromosomes in the GnomAD database, including 2,425 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2425 hom., cov: 32)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.12
• Publications: 3 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014361.4. 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
	CNTN5	NM_014361.4	MANE Select	c.55+39202C>G		intron	N/A	NP_055176.1	O94779-1
	CNTN5	NM_001243270.2		c.55+39202C>G		intron	N/A	NP_001230199.1	O94779-1
	CNTN5	NM_175566.2		c.55+39202C>G		intron	N/A	NP_780775.1	O94779-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN5	ENST00000524871.6	TSL:1 MANE Select	c.55+39202C>G		intron	N/A	ENSP00000435637.1	O94779-1
	CNTN5	ENST00000418526.6	TSL:1	c.55+39202C>G		intron	N/A	ENSP00000393229.2	O94779-2
	CNTN5	ENST00000527185.5	TSL:1	c.55+39202C>G		intron	N/A	ENSP00000433575.1	O94779-4

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24598 AN: 151750 Hom.: 2420 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0992

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0946

Gnomad OTH AF: 0.155

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.162 AC: 24623 AN: 151870 Hom.: 2425 Cov.: 32 AF XY: 0.164 AC XY: 12200 AN XY: 74218

African (AFR) AF: 0.268 AC: 11110 AN: 41422

American (AMR) AF: 0.143 AC: 2175 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0992 AC: 344 AN: 3468

East Asian (EAS) AF: 0.279 AC: 1436 AN: 5146

South Asian (SAS) AF: 0.236 AC: 1138 AN: 4816

European-Finnish (FIN) AF: 0.146 AC: 1538 AN: 10528

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0946 AC: 6426 AN: 67922

Other (OTH) AF: 0.157 AC: 331 AN: 2102

Alfa AF: 0.130 Hom.: 202

Bravo AF: 0.169

Asia WGS AF: 0.224 AC: 771 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.070
DANN	Benign	0.68
PhyloP100		-3.1
Mutation Taster		=100/0	polymorphism (auto)

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: rs10501918; hg19: chr11-99466202;