NM_014361.4:c.55+64537C>T

Variant names:

• chr11-99620806-C-T
• rs12807920
• NM_014361.4:c.55+64537C>T

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+64537C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,742 control chromosomes in the GnomAD database, including 15,927 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 0.45 (15927 hom., cov: 31)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.55+64537C>T		intron_variant	Intron 3 of 24	ENST00000524871.6	NP_055176.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN5	ENST00000524871.6	c.55+64537C>T		intron_variant	Intron 3 of 24	1	NM_014361.4	ENSP00000435637.1

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68503 AN: 151624 Hom.: 15904 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.452 AC: 68567 AN: 151742 Hom.: 15927 Cov.: 31 AF XY: 0.453 AC XY: 33595 AN XY: 74140

African (AFR) AF: 0.339 AC: 14051 AN: 41392

American (AMR) AF: 0.593 AC: 9038 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1746 AN: 3464

East Asian (EAS) AF: 0.532 AC: 2746 AN: 5164

South Asian (SAS) AF: 0.454 AC: 2185 AN: 4816

European-Finnish (FIN) AF: 0.428 AC: 4458 AN: 10414

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32687 AN: 67920

Other (OTH) AF: 0.460 AC: 971 AN: 2112

Alfa AF: 0.477 Hom.: 3105

Bravo AF: 0.458

Asia WGS AF: 0.506 AC: 1760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.30
PhyloP100		-0.11
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: rs12807920; hg19: chr11-99491537;