rs6590589

Variant names:

• chr11-100092328-G-A
• rs6590589
• NM_014361.4:c.1580+18034G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_014361.4(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 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• 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]

LOC105369456 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.1580+18034G>A		intron_variant	Intron 13 of 24	ENST00000524871.6	NP_055176.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN5	ENST00000524871.6	c.1580+18034G>A		intron_variant	Intron 13 of 24	1	NM_014361.4	ENSP00000435637.1

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

African (AFR) AF: 0.694 AC: 28769 AN: 41462

American (AMR) AF: 0.306 AC: 4656 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1423 AN: 3460

East Asian (EAS) AF: 0.388 AC: 1992 AN: 5132

South Asian (SAS) AF: 0.473 AC: 2279 AN: 4820

European-Finnish (FIN) AF: 0.360 AC: 3794 AN: 10534

Middle Eastern (MID) AF: 0.431 AC: 125 AN: 290

European-Non Finnish (NFE) AF: 0.321 AC: 21782 AN: 67926

Other (OTH) AF: 0.397 AC: 836 AN: 2106

Alfa AF: 0.397 Hom.: 1967

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
PhyloP100		-0.0060
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: rs6590589; hg19: chr11-99963060;