rs1216170

Variant names:

• chr11-100316148-A-C
• rs1216170
• NM_014361.4:c.2730+7680A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-100316148-A-C
• chr11-100316148-A-G
• chr11-100316148-A-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.2730+7680A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 152,080 control chromosomes in the GnomAD database, including 21,028 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 0.49 (21028 hom., cov: 33)
• Consequence: CNTN5 NM_014361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTN5	NM_014361.4	c.2730+7680A>C		intron_variant	Intron 21 of 24	ENST00000524871.6	NP_055176.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTN5	ENST00000524871.6	c.2730+7680A>C		intron_variant	Intron 21 of 24	1	NM_014361.4	ENSP00000435637.1

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74617 AN: 151962 Hom.: 20976 Cov.: 33

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.491 AC: 74720 AN: 152080 Hom.: 21028 Cov.: 33 AF XY: 0.500 AC XY: 37155 AN XY: 74310

African (AFR) AF: 0.722 AC: 29975 AN: 41506

American (AMR) AF: 0.555 AC: 8490 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1406 AN: 3470

East Asian (EAS) AF: 0.921 AC: 4758 AN: 5168

South Asian (SAS) AF: 0.510 AC: 2463 AN: 4826

European-Finnish (FIN) AF: 0.390 AC: 4113 AN: 10544

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22089 AN: 67966

Other (OTH) AF: 0.499 AC: 1052 AN: 2108

Alfa AF: 0.398 Hom.: 41262

Bravo AF: 0.519

Asia WGS AF: 0.722 AC: 2514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.4
DANN	Benign	0.76
PhyloP100		-0.28
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: rs1216170; hg19: chr11-100186880;