rs648519

Variant names:

• chr11-99596995-A-G
• rs648519
• NM_014361.4:c.55+40726A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-99596995-A-G
• chr11-99596995-A-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.55+40726A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,086 control chromosomes in the GnomAD database, including 5,016 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 0.25 (5016 hom., cov: 32)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.55+40726A>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+40726A>G		intron_variant	Intron 3 of 24	1	NM_014361.4	ENSP00000435637.1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38065 AN: 151968 Hom.: 5017 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.250 AC: 38078 AN: 152086 Hom.: 5016 Cov.: 32 AF XY: 0.246 AC XY: 18279 AN XY: 74344

African (AFR) AF: 0.199 AC: 8265 AN: 41514

American (AMR) AF: 0.242 AC: 3703 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1146 AN: 3470

East Asian (EAS) AF: 0.131 AC: 677 AN: 5176

South Asian (SAS) AF: 0.126 AC: 607 AN: 4818

European-Finnish (FIN) AF: 0.242 AC: 2550 AN: 10556

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19994 AN: 67964

Other (OTH) AF: 0.267 AC: 564 AN: 2110

Alfa AF: 0.284 Hom.: 18244

Bravo AF: 0.252

Asia WGS AF: 0.131 AC: 456 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.55
PhyloP100		-0.41
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: rs648519; hg19: chr11-99467726;