chr11-99584330-G-A

Position:

• chr11-99584330-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014361.4(CNTN5):​c.55+28061G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 151,998 control chromosomes in the GnomAD database, including 37,111 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 0.66 (37111 hom., cov: 31)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.55+28061G>A		intron_variant		ENST00000524871.6	NP_055176.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNTN5	ENST00000524871.6	c.55+28061G>A		intron_variant		1	NM_014361.4	ENSP00000435637	P1

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99971 AN: 151880 Hom.: 37096 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.658 AC: 100009 AN: 151998 Hom.: 37111 Cov.: 31 AF XY: 0.663 AC XY: 49266 AN XY: 74296

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.694

Alfa AF: 0.788 Hom.: 103535

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.6
DANN	Benign	0.26

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2726355; hg19: chr11-99455061;