rs1494471

Variant names:

• chr11-99559065-G-A
• rs1494471
• NM_014361.4:c.55+2796G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-99559065-G-A
• chr11-99559065-G-C
• chr11-99559065-G-T

Variant summary

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

The NM_014361.4(CNTN5):​c.55+2796G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,674 control chromosomes in the GnomAD database, including 7,203 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 0.30 (7203 hom., cov: 32)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.55+2796G>A		intron_variant	Intron 3 of 24	ENST00000524871.6	NP_055176.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN5	ENST00000524871.6	c.55+2796G>A		intron_variant	Intron 3 of 24	1	NM_014361.4	ENSP00000435637.1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45388 AN: 151556 Hom.: 7199 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.0243

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.299 AC: 45418 AN: 151674 Hom.: 7203 Cov.: 32 AF XY: 0.291 AC XY: 21569 AN XY: 74090

African (AFR) AF: 0.278 AC: 11499 AN: 41374

American (AMR) AF: 0.279 AC: 4255 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1367 AN: 3468

East Asian (EAS) AF: 0.0242 AC: 125 AN: 5174

South Asian (SAS) AF: 0.135 AC: 650 AN: 4800

European-Finnish (FIN) AF: 0.278 AC: 2927 AN: 10512

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.343 AC: 23253 AN: 67814

Other (OTH) AF: 0.328 AC: 690 AN: 2106

Alfa AF: 0.273 Hom.: 2022

Bravo AF: 0.304

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.22
PhyloP100		-0.61
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: rs1494471; hg19: chr11-99429796;