NM_014361.4:c.-70-79152T>A

Variant names:

• chr11-99476993-T-A
• rs2726363
• NM_014361.4:c.-70-79152T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014361.4(CNTN5):​c.-70-79152T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 151,614 control chromosomes in the GnomAD database, including 42,888 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 0.75 (42888 hom., cov: 30)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.-70-79152T>A		intron_variant	Intron 2 of 24	ENST00000524871.6	NP_055176.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN5	ENST00000524871.6	c.-70-79152T>A		intron_variant	Intron 2 of 24	1	NM_014361.4	ENSP00000435637.1
CNTN5	ENST00000527185.5	c.-70-79152T>A		intron_variant	Intron 2 of 20	1		ENSP00000433575.1
CNTN5	ENST00000528727.5	n.435-79152T>A		intron_variant	Intron 2 of 15	1
CNTN5	ENST00000528682.5	c.-70-79152T>A		intron_variant	Intron 1 of 23	5		ENSP00000436185.1

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113340 AN: 151496 Hom.: 42862 Cov.: 30

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.748 AC: 113411 AN: 151614 Hom.: 42888 Cov.: 30 AF XY: 0.742 AC XY: 54936 AN XY: 74040

African (AFR) AF: 0.672 AC: 27760 AN: 41330

American (AMR) AF: 0.847 AC: 12893 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.854 AC: 2963 AN: 3468

East Asian (EAS) AF: 0.500 AC: 2571 AN: 5138

South Asian (SAS) AF: 0.686 AC: 3305 AN: 4816

European-Finnish (FIN) AF: 0.702 AC: 7348 AN: 10460

Middle Eastern (MID) AF: 0.862 AC: 250 AN: 290

European-Non Finnish (NFE) AF: 0.796 AC: 54052 AN: 67864

Other (OTH) AF: 0.788 AC: 1665 AN: 2112

Alfa AF: 0.770 Hom.: 5315

Bravo AF: 0.757

Asia WGS AF: 0.553 AC: 1923 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.38
PhyloP100		-0.053
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: rs2726363; hg19: chr11-99347724; COSMIC: COSV73150390;