rs10501940

Positions:

• chr11-100064136-G-C

Variant summary

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

The NM_014361.4(CNTN5):​c.1162+2743G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,082 control chromosomes in the GnomAD database, including 1,468 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 0.13 (1468 hom., cov: 32)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730

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]

LOC105369456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTN5	NM_014361.4	c.1162+2743G>C		intron_variant		ENST00000524871.6
LOC105369456	XR_947948.3	n.208-8606C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTN5	ENST00000524871.6	c.1162+2743G>C		intron_variant		1	NM_014361.4	P1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20300 AN: 151962 Hom.: 1468 Cov.: 32

Gnomad AFR AF: 0.0790

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.0592

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.134 AC: 20305 AN: 152082 Hom.: 1468 Cov.: 32 AF XY: 0.136 AC XY: 10119 AN XY: 74332

Gnomad4 AFR AF: 0.0788

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.0594

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.156

Alfa AF: 0.148 Hom.: 220

Bravo AF: 0.127

Asia WGS AF: 0.0890 AC: 311 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	0.23
DANN	Benign	0.45

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501940; hg19: chr11-99934868;