11-100356042-A-T

Variant names:

• chr11-100356042-A-T
• rs10894795
• NM_014361.4:c.3200-75A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000524871.6(CNTN5):​c.3200-75A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CNTN5 ENST00000524871.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.964
• Publications: 8 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524871.6. 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.3200-75A>T		intron	N/A	NP_055176.1
	CNTN5	NM_001243270.2		c.3200-75A>T		intron	N/A	NP_001230199.1
	CNTN5	NM_175566.2		c.2978-75A>T		intron	N/A	NP_780775.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTN5	ENST00000524871.6	TSL:1 MANE Select	c.3200-75A>T		intron	N/A	ENSP00000435637.1
	CNTN5	ENST00000418526.6	TSL:1	c.2978-75A>T		intron	N/A	ENSP00000393229.2
	CNTN5	ENST00000528682.5	TSL:5	c.3200-75A>T		intron	N/A	ENSP00000436185.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 769990 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 403076

African (AFR) AF: 0.00 AC: 0 AN: 18962

American (AMR) AF: 0.00 AC: 0 AN: 34956

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21008

East Asian (EAS) AF: 0.00 AC: 0 AN: 33224

South Asian (SAS) AF: 0.00 AC: 0 AN: 66546

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47798

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4488

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 505666

Other (OTH) AF: 0.00 AC: 0 AN: 37342

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 10572

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.71
PhyloP100		0.96

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: rs10894795; hg19: chr11-100226773;