11-99071142-A-G

Variant names:

• chr11-99071142-A-G
• rs1940484
• NM_014361.4:c.-210+49872A>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.-210+49872A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,848 control chromosomes in the GnomAD database, including 11,537 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 0.39 (11537 hom., cov: 31)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 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.-210+49872A>G		intron	N/A	NP_055176.1	O94779-1
	CNTN5	NM_001243270.2		c.-71+49872A>G		intron	N/A	NP_001230199.1	O94779-1
	CNTN5	NM_001243271.2		c.-210+49872A>G		intron	N/A	NP_001230200.1	O94779-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN5	ENST00000524871.6	TSL:1 MANE Select	c.-210+49872A>G		intron	N/A	ENSP00000435637.1	O94779-1
	CNTN5	ENST00000527185.5	TSL:1	c.-210+49872A>G		intron	N/A	ENSP00000433575.1	O94779-4
	CNTN5	ENST00000528727.5	TSL:1	n.295+49872A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58448 AN: 151732 Hom.: 11520 Cov.: 31

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.385 AC: 58501 AN: 151848 Hom.: 11537 Cov.: 31 AF XY: 0.390 AC XY: 28937 AN XY: 74214

African (AFR) AF: 0.429 AC: 17763 AN: 41398

American (AMR) AF: 0.445 AC: 6780 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1233 AN: 3466

East Asian (EAS) AF: 0.543 AC: 2801 AN: 5162

South Asian (SAS) AF: 0.456 AC: 2198 AN: 4820

European-Finnish (FIN) AF: 0.365 AC: 3850 AN: 10548

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22636 AN: 67906

Other (OTH) AF: 0.412 AC: 866 AN: 2104

Alfa AF: 0.354 Hom.: 42028

Bravo AF: 0.394

Asia WGS AF: 0.533 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.033
DANN	Benign	0.42
PhyloP100		-2.4
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: rs1940484; hg19: chr11-98941872;