rs6590589

Positions:

• chr11-100092328-G-A
• chr11-100092328-G-C

Variant summary

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

The ENST00000524871.6(CNTN5):​c.1580+18034G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,878 control chromosomes in the GnomAD database, including 16,384 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 0.44 (16384 hom., cov: 32)
• Consequence: CNTN5 ENST00000524871.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.1580+18034G>A		intron_variant		ENST00000524871.6	NP_055176.1
LOC105369456	XR_947948.3	n.207+13707C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNTN5	ENST00000524871.6	c.1580+18034G>A		intron_variant		1	NM_014361.4	ENSP00000435637	P1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65980 AN: 151760 Hom.: 16335 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.435 AC: 66078 AN: 151878 Hom.: 16384 Cov.: 32 AF XY: 0.434 AC XY: 32167 AN XY: 74194

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.397

Alfa AF: 0.387 Hom.: 1791

Bravo AF: 0.440

Asia WGS AF: 0.413 AC: 1436 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.6
DANN	Benign	0.46

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

Publications

LitVar

Other links and lift over

dbSNP: rs6590589; hg19: chr11-99963060;