chr11-99982441-A-C

Variant names:

• chr11-99982441-A-C
• rs6590474
• NM_014361.4:c.878-19593A>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.878-19593A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 151,948 control chromosomes in the GnomAD database, including 39,009 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 0.71 (39009 hom., cov: 31)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.878-19593A>C		intron_variant	Intron 8 of 24	ENST00000524871.6	NP_055176.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN5	ENST00000524871.6	c.878-19593A>C		intron_variant	Intron 8 of 24	1	NM_014361.4	ENSP00000435637.1

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108124 AN: 151830 Hom.: 38974 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.712 AC: 108216 AN: 151948 Hom.: 39009 Cov.: 31 AF XY: 0.709 AC XY: 52673 AN XY: 74272

African (AFR) AF: 0.824 AC: 34146 AN: 41432

American (AMR) AF: 0.728 AC: 11123 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2534 AN: 3468

East Asian (EAS) AF: 0.804 AC: 4146 AN: 5154

South Asian (SAS) AF: 0.649 AC: 3118 AN: 4808

European-Finnish (FIN) AF: 0.627 AC: 6608 AN: 10540

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44208 AN: 67944

Other (OTH) AF: 0.693 AC: 1464 AN: 2114

Alfa AF: 0.695 Hom.: 16044

Bravo AF: 0.729

Asia WGS AF: 0.684 AC: 2377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.53
PhyloP100		-1.3
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

Publications

LitVar

Other links and lift over

dbSNP: rs6590474; hg19: chr11-99853173;