11-100002678-T-C

Variant names:

• chr11-100002678-T-C
• rs7947224
• NM_014361.4:c.980+542T>C

Variant summary

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

The NM_014361.4(CNTN5):​c.980+542T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151,960 control chromosomes in the GnomAD database, including 12,327 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 0.38 (12327 hom., cov: 32)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.06
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.58 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.980+542T>C		intron	N/A	NP_055176.1
	CNTN5	NM_001243270.2		c.980+542T>C		intron	N/A	NP_001230199.1
	CNTN5	NM_175566.2		c.758+542T>C		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.980+542T>C		intron	N/A	ENSP00000435637.1
	CNTN5	ENST00000418526.6	TSL:1	c.758+542T>C		intron	N/A	ENSP00000393229.2
	CNTN5	ENST00000527185.5	TSL:1	c.980+542T>C		intron	N/A	ENSP00000433575.1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57327 AN: 151842 Hom.: 12311 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.378 AC: 57385 AN: 151960 Hom.: 12327 Cov.: 32 AF XY: 0.371 AC XY: 27594 AN XY: 74278

African (AFR) AF: 0.586 AC: 24275 AN: 41434

American (AMR) AF: 0.314 AC: 4786 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1323 AN: 3472

East Asian (EAS) AF: 0.112 AC: 577 AN: 5168

South Asian (SAS) AF: 0.306 AC: 1475 AN: 4826

European-Finnish (FIN) AF: 0.259 AC: 2742 AN: 10580

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20947 AN: 67920

Other (OTH) AF: 0.365 AC: 767 AN: 2104

Alfa AF: 0.359 Hom.: 1344

Bravo AF: 0.391

Asia WGS AF: 0.237 AC: 823 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.027
DANN	Benign	0.37
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: rs7947224; hg19: chr11-99873410;