3-2542692-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_175607.3(CNTN4):c.-88-28724G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0407 in 152,210 control chromosomes in the GnomAD database, including 185 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.041 (185 hom., cov: 32)
• Consequence: CNTN4 NM_175607.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0690

Genes affected

CNTN4 (HGNC:2174): (contactin 4) This gene encodes a member of the contactin family of immunoglobulins. Contactins are axon-associated cell adhesion molecules that function in neuronal network formation and plasticity. The encoded protein is a glycosylphosphatidylinositol-anchored neuronal membrane protein that may play a role in the formation of axon connections in the developing nervous system. Deletion or mutation of this gene may play a role in 3p deletion syndrome and autism spectrum disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BP6: Variant 3-2542692-G-T is Benign according to our data. Variant chr3-2542692-G-T is described in ClinVar as [Benign]. Clinvar id is 1241762.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTN4	NM_175607.3	c.-88-28724G>T		intron_variant		ENST00000418658.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTN4	ENST00000418658.6	c.-88-28724G>T		intron_variant		5	NM_175607.3	P1

Frequencies

GnomAD3 genomes AF: 0.0407 AC: 6195 AN: 152092 Hom.: 185 Cov.: 32

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.0248

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00703

Gnomad FIN AF: 0.0864

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0612

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0407 AC: 6192 AN: 152210 Hom.: 185 Cov.: 32 AF XY: 0.0406 AC XY: 3019 AN XY: 74416

Gnomad4 AFR AF: 0.0107

Gnomad4 AMR AF: 0.0246

Gnomad4 ASJ AF: 0.0346

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00704

Gnomad4 FIN AF: 0.0864

Gnomad4 NFE AF: 0.0612

Gnomad4 OTH AF: 0.0313

Alfa AF: 0.0513 Hom.: 295

Bravo AF: 0.0348

Asia WGS AF: 0.00491 AC: 17 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 10, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	15
Dann	Benign	0.71

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: rs7649181; hg19: chr3-2584376;