11-99886997-T-G

Variant names:

• chr11-99886997-T-G
• rs10501927
• NM_014361.4:c.578-29057T>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.578-29057T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,190 control chromosomes in the GnomAD database, including 2,167 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 0.16 (2167 hom., cov: 33)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 11 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN5	NM_014361.4	MANE Select	c.578-29057T>G		intron	N/A	NP_055176.1
	CNTN5	NM_001243270.2		c.578-29057T>G		intron	N/A	NP_001230199.1
	CNTN5	NM_175566.2		c.356-29057T>G		intron	N/A	NP_780775.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN5	ENST00000524871.6	TSL:1 MANE Select	c.578-29057T>G		intron	N/A	ENSP00000435637.1
	CNTN5	ENST00000418526.6	TSL:1	c.356-29057T>G		intron	N/A	ENSP00000393229.2
	CNTN5	ENST00000527185.5	TSL:1	c.578-29057T>G		intron	N/A	ENSP00000433575.1

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24673 AN: 152072 Hom.: 2163 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.162 AC: 24686 AN: 152190 Hom.: 2167 Cov.: 33 AF XY: 0.158 AC XY: 11753 AN XY: 74414

African (AFR) AF: 0.126 AC: 5250 AN: 41520

American (AMR) AF: 0.136 AC: 2086 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 784 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.126 AC: 605 AN: 4818

European-Finnish (FIN) AF: 0.156 AC: 1652 AN: 10602

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13674 AN: 67988

Other (OTH) AF: 0.175 AC: 369 AN: 2112

Alfa AF: 0.180 Hom.: 1971

Bravo AF: 0.161

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.35
PhyloP100		-0.11
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: rs10501927; hg19: chr11-99757729;