11-99715005-G-A

Variant names:

• chr11-99715005-G-A
• rs952700
• NM_014361.4:c.56-104539G>A

Variant summary

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

The NM_014361.4(CNTN5):​c.56-104539G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,658 control chromosomes in the GnomAD database, including 6,225 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 0.28 (6225 hom., cov: 32)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.685
• Publications: 13 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 (SAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.56-104539G>A		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.56-104539G>A		intron_variant	Intron 3 of 24	1	NM_014361.4	ENSP00000435637.1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43160 AN: 151540 Hom.: 6232 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.285 AC: 43173 AN: 151658 Hom.: 6225 Cov.: 32 AF XY: 0.287 AC XY: 21274 AN XY: 74124

African (AFR) AF: 0.265 AC: 10971 AN: 41394

American (AMR) AF: 0.323 AC: 4919 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1208 AN: 3468

East Asian (EAS) AF: 0.304 AC: 1546 AN: 5090

South Asian (SAS) AF: 0.340 AC: 1634 AN: 4810

European-Finnish (FIN) AF: 0.327 AC: 3434 AN: 10508

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.273 AC: 18525 AN: 67860

Other (OTH) AF: 0.321 AC: 678 AN: 2110

Alfa AF: 0.280 Hom.: 22697

Bravo AF: 0.285

Asia WGS AF: 0.299 AC: 1035 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.81
DANN	Benign	0.83
PhyloP100		-0.69
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: rs952700; hg19: chr11-99585736;