11-99168926-C-T

Variant names:

• chr11-99168926-C-T
• rs11218615
• NM_014361.4:c.-210+147656C>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.-210+147656C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,072 control chromosomes in the GnomAD database, including 15,004 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 0.43 (15004 hom., cov: 33)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.-210+147656C>T		intron_variant	Intron 1 of 24	ENST00000524871.6	NP_055176.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN5	ENST00000524871.6	c.-210+147656C>T		intron_variant	Intron 1 of 24	1	NM_014361.4	ENSP00000435637.1
CNTN5	ENST00000527185.5	c.-210+147656C>T		intron_variant	Intron 1 of 20	1		ENSP00000433575.1
CNTN5	ENST00000528727.5	n.295+147656C>T		intron_variant	Intron 1 of 15	1
CNTN5	ENST00000528682.5	c.-71+147656C>T		intron_variant	Intron 1 of 23	5		ENSP00000436185.1

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65537 AN: 151954 Hom.: 14992 Cov.: 33

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.431 AC: 65579 AN: 152072 Hom.: 15004 Cov.: 33 AF XY: 0.441 AC XY: 32769 AN XY: 74334

African (AFR) AF: 0.317 AC: 13139 AN: 41484

American (AMR) AF: 0.511 AC: 7815 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1492 AN: 3468

East Asian (EAS) AF: 0.805 AC: 4156 AN: 5164

South Asian (SAS) AF: 0.524 AC: 2527 AN: 4818

European-Finnish (FIN) AF: 0.503 AC: 5325 AN: 10584

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.437 AC: 29725 AN: 67958

Other (OTH) AF: 0.438 AC: 926 AN: 2112

Alfa AF: 0.345 Hom.: 1682

Bravo AF: 0.425

Asia WGS AF: 0.621 AC: 2158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.66
PhyloP100		-0.36
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: rs11218615; hg19: chr11-99039657;