rs278906

chr12-41024835-T-Cchr12-41024835-T-G

Variant summary

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

The NM_001843.4(CNTN1):c.2524-315T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,188 control chromosomes in the GnomAD database, including 1,295 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 0.10 (1295 hom., cov: 32)
• Consequence: CNTN1 NM_001843.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175

Genes affected

CNTN1 (HGNC:2171): (contactin 1) The protein encoded by this gene is a member of the immunoglobulin superfamily. It 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. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTN1	NM_001843.4	c.2524-315T>C		intron_variant		ENST00000551295.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTN1	ENST00000551295.7	c.2524-315T>C		intron_variant		1	NM_001843.4	P3
CNTN1	ENST00000347616.5	c.2524-315T>C		intron_variant		1		P3
CNTN1	ENST00000348761.2	c.2491-315T>C		intron_variant		1		A1
CNTN1	ENST00000550305.1	n.483-315T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15247 AN: 152070 Hom.: 1292 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.0354

Gnomad EAS AF: 0.0194

Gnomad SAS AF: 0.0356

Gnomad FIN AF: 0.0838

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0515

Gnomad OTH AF: 0.0776

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

GnomAD4 genome AF: 0.100 AC: 15270 AN: 152188 Hom.: 1295 Cov.: 32 AF XY: 0.0986 AC XY: 7334 AN XY: 74416

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.0544

Gnomad4 ASJ AF: 0.0354

Gnomad4 EAS AF: 0.0195

Gnomad4 SAS AF: 0.0356

Gnomad4 FIN AF: 0.0838

Gnomad4 NFE AF: 0.0515

Gnomad4 OTH AF: 0.0768

Alfa AF: 0.0393 Hom.: 38

Bravo AF: 0.103

Asia WGS AF: 0.0490 AC: 169 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	14
Dann	Benign	0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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: rs278906; hg19: chr12-41418637;