9-41898902-C-A

Position:

• chr9-41898902-C-A

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4

The NM_001201380.3(CNTNAP3B):​c.3540G>T​(p.Lys1180Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 0)
• Consequence: CNTNAP3B NM_001201380.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.273

Genes affected

CNTNAP3B (HGNC:32035): (contactin associated protein family member 3B) Predicted to be involved in cell adhesion. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.29344028).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTNAP3B	NM_001201380.3	c.3540G>T	p.Lys1180Asn	missense_variant	22/24	ENST00000377561.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTNAP3B	ENST00000377561.7	c.3540G>T	p.Lys1180Asn	missense_variant	22/24	1	NM_001201380.3	P1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 10, 2021

The c.3540G>T (p.K1180N) alteration is located in exon 22 (coding exon 22) of the CNTNAP3B gene. This alteration results from a G to T substitution at nucleotide position 3540, causing the lysine (K) at amino acid position 1180 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.95
BayesDel_noAF	Benign	-0.52
CADD	Uncertain	24
DANN	Benign	0.94
DEOGEN2	Benign	0.18	.;T
LIST_S2	Uncertain	0.93	D;D
MetaRNN	Benign	0.29	T;T
Sift4G	Pathogenic	0.0010	D;D
Vest4		0.46
gMVP		0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-65657060;