Variant chr9-41894062-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001201380.3(CNTNAP3B):c.3794C>A(p.Ala1265Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 1)

Exomes 𝑓: 0.000014 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CNTNAP3B
NM_001201380.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.88

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNTNAP3B	NM_001201380.3 linkuse as main transcript	c.3794C>A	p.Ala1265Asp	missense_variant	24/24	ENST00000377561.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNTNAP3B	ENST00000377561.7 linkuse as main transcript	c.3794C>A	p.Ala1265Asp	missense_variant	24/24	1	NM_001201380.3	P1	Q96NU0-1
CNTNAP3B	ENST00000612828.4 linkuse as main transcript	c.3551C>A	p.Ala1184Asp	missense_variant	23/23	1
CNTNAP3B	ENST00000476961.5 linkuse as main transcript	c.470C>A	p.Ala157Asp	missense_variant	5/5	1
CNTNAP3B	ENST00000619138.4 linkuse as main transcript	c.*558C>A		3_prime_UTR_variant, NMD_transcript_variant	22/22	1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000137

AC:

AN:

73130

Hom.:

Cov.:

AF XY:

0.0000248

AC XY:

AN XY:

40338

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000241

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 07, 2023

The c.3794C>A (p.A1265D) alteration is located in exon 24 (coding exon 24) of the CNTNAP3B gene. This alteration results from a C to A substitution at nucleotide position 3794, causing the alanine (A) at amino acid position 1265 to be replaced by an aspartic acid (D). 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

0.60

BayesDel_noAF

Benign

-0.70

CADD

Benign

DANN

Benign

0.82

DEOGEN2

Benign

0.078

.;T

LIST_S2

Uncertain

0.95

D;D

MetaRNN

Uncertain

0.63

D;D

Sift4G

Uncertain

0.049

D;D

Vest4

0.66

gMVP

0.68

Splicing

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

Publications

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over