rs10894157

Variant names:

• chr11-99913301-A-G
• rs10894157
• NM_014361.4:c.578-2753A>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.578-2753A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,974 control chromosomes in the GnomAD database, including 3,489 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 0.21 (3489 hom., cov: 32)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN5	NM_014361.4	MANE Select	c.578-2753A>G		intron	N/A	NP_055176.1
	CNTN5	NM_001243270.2		c.578-2753A>G		intron	N/A	NP_001230199.1
	CNTN5	NM_175566.2		c.356-2753A>G		intron	N/A	NP_780775.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN5	ENST00000524871.6	TSL:1 MANE Select	c.578-2753A>G		intron	N/A	ENSP00000435637.1
	CNTN5	ENST00000418526.6	TSL:1	c.356-2753A>G		intron	N/A	ENSP00000393229.2
	CNTN5	ENST00000527185.5	TSL:1	c.578-2753A>G		intron	N/A	ENSP00000433575.1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31716 AN: 151854 Hom.: 3490 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.209 AC: 31715 AN: 151974 Hom.: 3489 Cov.: 32 AF XY: 0.202 AC XY: 15016 AN XY: 74304

African (AFR) AF: 0.251 AC: 10416 AN: 41470

American (AMR) AF: 0.156 AC: 2372 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3470

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5170

South Asian (SAS) AF: 0.148 AC: 715 AN: 4830

European-Finnish (FIN) AF: 0.166 AC: 1762 AN: 10588

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15002 AN: 67906

Other (OTH) AF: 0.203 AC: 427 AN: 2104

Alfa AF: 0.214 Hom.: 595

Bravo AF: 0.209

Asia WGS AF: 0.0740 AC: 259 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.61
DANN	Benign	0.76
PhyloP100		-0.26
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: rs10894157; hg19: chr11-99784033;