rs1596516

chr12-40810126-A-Gchr12-40810126-A-T

Variant summary

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

The NM_001843.4(CNTN1):c.-76-98231A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,980 control chromosomes in the GnomAD database, including 24,363 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 (24363 hom., cov: 32)
• Consequence: CNTN1 NM_001843.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTN1	NM_001843.4	c.-76-98231A>G		intron_variant		ENST00000551295.7
CNTN1	NM_001256063.2	c.-76-98231A>G		intron_variant
CNTN1	XM_011537926.4	c.-77+46928A>G		intron_variant
CNTN1	XM_024448843.2	c.-77+46928A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTN1	ENST00000551295.7	c.-76-98231A>G		intron_variant		1	NM_001843.4	P3

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85242 AN: 151862 Hom.: 24325 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.561 AC: 85317 AN: 151980 Hom.: 24363 Cov.: 32 AF XY: 0.565 AC XY: 41989 AN XY: 74274

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.563

Alfa AF: 0.553 Hom.: 4837

Bravo AF: 0.566

Asia WGS AF: 0.651 AC: 2259 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.6
Dann	Benign	0.73

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: rs1596516; hg19: chr12-41203928;