rs312273

chr12-40853940-G-Achr12-40853940-G-Cchr12-40853940-G-T

Variant summary

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

The NM_001843.4(CNTN1):c.-76-54417G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 150,186 control chromosomes in the GnomAD database, including 25,152 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 0.56 (25152 hom., cov: 27)
• Consequence: CNTN1 NM_001843.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.482

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTN1	NM_001843.4	c.-76-54417G>A		intron_variant		ENST00000551295.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTN1	ENST00000551295.7	c.-76-54417G>A		intron_variant		1	NM_001843.4	P3

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84023 AN: 150068 Hom.: 25115 Cov.: 27

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.560 AC: 84100 AN: 150186 Hom.: 25152 Cov.: 27 AF XY: 0.559 AC XY: 40957 AN XY: 73214

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.527

Alfa AF: 0.517 Hom.: 3503

Bravo AF: 0.569

Asia WGS AF: 0.429 AC: 1495 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.7
Dann	Benign	0.29

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: rs312273; hg19: chr12-41247742;