rs2406918

Positions:

• chr11-99325420-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014361.4(CNTN5):​c.-135G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,908 control chromosomes in the GnomAD database, including 7,569 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 0.31 (7569 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CNTN5 NM_014361.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.42

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]

CNTN5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.-135G>T		5_prime_UTR_variant	2/25	ENST00000524871.6	NP_055176.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNTN5	ENST00000524871	c.-135G>T		5_prime_UTR_variant	2/25	1	NM_014361.4	ENSP00000435637.1
CNTN5	ENST00000527185	c.-135G>T		5_prime_UTR_variant	2/21	1		ENSP00000433575.1
CNTN5	ENST00000528727.5	n.370G>T		non_coding_transcript_exon_variant	2/16	1
CNTN5	ENST00000528682.5	c.-70-230725G>T		intron_variant		5		ENSP00000436185.1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47736 AN: 151794 Hom.: 7568 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.345

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 ASJ exome AF: 0.00

GnomAD4 genome AF: 0.314 AC: 47753 AN: 151908 Hom.: 7569 Cov.: 32 AF XY: 0.306 AC XY: 22695 AN XY: 74214

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.346

Alfa AF: 0.323 Hom.: 1168

Bravo AF: 0.312

Asia WGS AF: 0.308 AC: 1071 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	17
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2406918; hg19: chr11-99196151;