chr11-99631251-A-G

Variant names:

• chr11-99631251-A-G
• rs680914
• NM_014361.4:c.55+74982A>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+74982A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 151,896 control chromosomes in the GnomAD database, including 29,092 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 0.61 (29092 hom., cov: 31)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• 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]

LOC107984431 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.718 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.55+74982A>G		intron	N/A	NP_055176.1
	CNTN5	NM_001243270.2		c.55+74982A>G		intron	N/A	NP_001230199.1
	CNTN5	NM_175566.2		c.55+74982A>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.55+74982A>G		intron	N/A	ENSP00000435637.1
	CNTN5	ENST00000418526.6	TSL:1	c.55+74982A>G		intron	N/A	ENSP00000393229.2
	CNTN5	ENST00000527185.5	TSL:1	c.55+74982A>G		intron	N/A	ENSP00000433575.1

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92495 AN: 151778 Hom.: 29060 Cov.: 31

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.692

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.609 AC: 92577 AN: 151896 Hom.: 29092 Cov.: 31 AF XY: 0.609 AC XY: 45210 AN XY: 74216

African (AFR) AF: 0.456 AC: 18899 AN: 41422

American (AMR) AF: 0.729 AC: 11121 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2586 AN: 3464

East Asian (EAS) AF: 0.547 AC: 2818 AN: 5156

South Asian (SAS) AF: 0.544 AC: 2619 AN: 4814

European-Finnish (FIN) AF: 0.593 AC: 6256 AN: 10546

Middle Eastern (MID) AF: 0.686 AC: 199 AN: 290

European-Non Finnish (NFE) AF: 0.679 AC: 46130 AN: 67942

Other (OTH) AF: 0.641 AC: 1349 AN: 2106

Alfa AF: 0.597 Hom.: 5425

Bravo AF: 0.612

Asia WGS AF: 0.582 AC: 2014 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.64
DANN	Benign	0.54
PhyloP100		-0.084
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: rs680914; hg19: chr11-99501982;