rs10501920

Variant names:

• chr11-99622442-C-G
• rs10501920
• NM_014361.4:c.55+66173C>G

Variant summary

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

The NM_014361.4(CNTN5):​c.55+66173C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 151,898 control chromosomes in the GnomAD database, including 1,766 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 0.14 (1766 hom., cov: 32)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 12 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=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.55+66173C>G		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.55+66173C>G		intron_variant	Intron 3 of 24	1	NM_014361.4	ENSP00000435637.1

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21769 AN: 151780 Hom.: 1764 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0964

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.143 AC: 21787 AN: 151898 Hom.: 1766 Cov.: 32 AF XY: 0.146 AC XY: 10872 AN XY: 74220

African (AFR) AF: 0.215 AC: 8906 AN: 41436

American (AMR) AF: 0.0955 AC: 1458 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 346 AN: 3470

East Asian (EAS) AF: 0.207 AC: 1067 AN: 5152

South Asian (SAS) AF: 0.236 AC: 1138 AN: 4814

European-Finnish (FIN) AF: 0.181 AC: 1906 AN: 10538

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0964 AC: 6549 AN: 67922

Other (OTH) AF: 0.140 AC: 294 AN: 2102

Alfa AF: 0.118 Hom.: 159

Bravo AF: 0.141

Asia WGS AF: 0.202 AC: 702 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	3.3
DANN	Benign	0.45
PhyloP100		-0.16
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: rs10501920; hg19: chr11-99493173;