rs10784948

chr12-40917005-C-T

Variant summary

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

The NM_001843.4(CNTN1):c.95-1634C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 125,086 control chromosomes in the GnomAD database, including 1,188 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 0.15 (1188 hom., cov: 26)
• Consequence: CNTN1 NM_001843.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTN1	NM_001843.4	c.95-1634C>T		intron_variant		ENST00000551295.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTN1	ENST00000551295.7	c.95-1634C>T		intron_variant		1	NM_001843.4	P3

Frequencies

GnomAD3 genomes AF: 0.148 AC: 18460 AN: 125060 Hom.: 1188 Cov.: 26

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.0808

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.148 AC: 18469 AN: 125086 Hom.: 1188 Cov.: 26 AF XY: 0.152 AC XY: 8919 AN XY: 58512

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.0767

Gnomad4 SAS AF: 0.0812

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.143

Alfa AF: 0.123 Hom.: 252

Bravo AF: 0.123

Asia WGS AF: 0.0770 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.7
Dann	Benign	0.82

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: rs10784948; hg19: chr12-41310807;