rs10501943

chr11-100076267-T-C

Variant summary

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

The NM_014361.4(CNTN5):c.1580+1973T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,126 control chromosomes in the GnomAD database, including 2,250 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 0.17 (2250 hom., cov: 32)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTN5	NM_014361.4	c.1580+1973T>C		intron_variant		ENST00000524871.6
LOC105369456	XR_947948.3	n.208-20737A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTN5	ENST00000524871.6	c.1580+1973T>C		intron_variant		1	NM_014361.4	P1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25789 AN: 152008 Hom.: 2249 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.170 AC: 25795 AN: 152126 Hom.: 2250 Cov.: 32 AF XY: 0.171 AC XY: 12743 AN XY: 74350

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.0553

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.192

Alfa AF: 0.171 Hom.: 312

Bravo AF: 0.167

Asia WGS AF: 0.102 AC: 355 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.1
Dann	Benign	0.58

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: rs10501943; hg19: chr11-99946999;