rs11219732

Variant names:

• chr11-99387094-C-T
• rs11219732
• NM_014361.4:c.-71+61610C>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.-71+61610C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0606 in 151,966 control chromosomes in the GnomAD database, including 674 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 0.061 (674 hom., cov: 32)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014361.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN5	NM_014361.4	MANE Select	c.-71+61610C>T		intron	N/A	NP_055176.1
	CNTN5	NM_001243270.2		c.-70-169051C>T		intron	N/A	NP_001230199.1
	CNTN5	NM_001243271.2		c.-71+61610C>T		intron	N/A	NP_001230200.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN5	ENST00000524871.6	TSL:1 MANE Select	c.-71+61610C>T		intron	N/A	ENSP00000435637.1
	CNTN5	ENST00000527185.5	TSL:1	c.-71+61610C>T		intron	N/A	ENSP00000433575.1
	CNTN5	ENST00000528727.5	TSL:1	n.434+61610C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0606 AC: 9198 AN: 151848 Hom.: 674 Cov.: 32

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0399

Gnomad OTH AF: 0.0484

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

GnomAD4 genome AF: 0.0606 AC: 9207 AN: 151966 Hom.: 674 Cov.: 32 AF XY: 0.0701 AC XY: 5204 AN XY: 74234

African (AFR) AF: 0.0119 AC: 492 AN: 41480

American (AMR) AF: 0.129 AC: 1964 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0228 AC: 79 AN: 3468

East Asian (EAS) AF: 0.335 AC: 1722 AN: 5136

South Asian (SAS) AF: 0.136 AC: 653 AN: 4818

European-Finnish (FIN) AF: 0.137 AC: 1439 AN: 10542

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0400 AC: 2716 AN: 67970

Other (OTH) AF: 0.0488 AC: 103 AN: 2110

Alfa AF: 0.0451 Hom.: 498

Bravo AF: 0.0585

Asia WGS AF: 0.200 AC: 695 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.37
PhyloP100		-0.77
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: rs11219732; hg19: chr11-99257825;