9-41898518-A-G

Position:

• chr9-41898518-A-G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001201380.3(CNTNAP3B):​c.3689T>C​(p.Val1230Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 6/7 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 0)
• Consequence: CNTNAP3B NM_001201380.3 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.226

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]

CNTNAP3B (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.06576714).
• BP6: Variant 9-41898518-A-G is Benign according to our data. Variant chr9-41898518-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2363036.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTNAP3B	NM_001201380.3	c.3689T>C	p.Val1230Ala	missense_variant	23/24	ENST00000377561.7	NP_001188309.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNTNAP3B	ENST00000377561.7	c.3689T>C	p.Val1230Ala	missense_variant	23/24	1	NM_001201380.3	ENSP00000478671.2

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 27, 2022

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.047
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.20
DANN	Benign	0.77
DEOGEN2	Benign	0.0026	.;T
LIST_S2	Benign	0.017	T;T
MetaRNN	Benign	0.066	T;T
Sift4G	Benign	0.86	T;T
Vest4		0.068
gMVP		0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1554733856; hg19: chr9-65657444;