chr11-100093237-A-G

Variant names:

• chr11-100093237-A-G
• rs10791161
• NM_014361.4:c.1580+18943A>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.1580+18943A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,758 control chromosomes in the GnomAD database, including 22,736 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 0.53 (22736 hom., cov: 31)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 4 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]

LOC105369456 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 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.1580+18943A>G		intron	N/A	NP_055176.1	O94779-1
	CNTN5	NM_001243270.2		c.1580+18943A>G		intron	N/A	NP_001230199.1	O94779-1
	CNTN5	NM_175566.2		c.1358+18943A>G		intron	N/A	NP_780775.1	O94779-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN5	ENST00000524871.6	TSL:1 MANE Select	c.1580+18943A>G		intron	N/A	ENSP00000435637.1	O94779-1
	CNTN5	ENST00000418526.6	TSL:1	c.1358+18943A>G		intron	N/A	ENSP00000393229.2	O94779-2
	CNTN5	ENST00000527185.5	TSL:1	c.1580+18943A>G		intron	N/A	ENSP00000433575.1	O94779-4

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81061 AN: 151640 Hom.: 22711 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.535 AC: 81129 AN: 151758 Hom.: 22736 Cov.: 31 AF XY: 0.537 AC XY: 39815 AN XY: 74142

African (AFR) AF: 0.670 AC: 27715 AN: 41394

American (AMR) AF: 0.474 AC: 7216 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1895 AN: 3460

East Asian (EAS) AF: 0.745 AC: 3812 AN: 5114

South Asian (SAS) AF: 0.628 AC: 3016 AN: 4802

European-Finnish (FIN) AF: 0.498 AC: 5256 AN: 10554

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.451 AC: 30618 AN: 67888

Other (OTH) AF: 0.516 AC: 1087 AN: 2108

Alfa AF: 0.485 Hom.: 58442

Bravo AF: 0.536

Asia WGS AF: 0.719 AC: 2501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.47
PhyloP100		-0.10
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: rs10791161; hg19: chr11-99963969;