2-124524333-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_001367498.1(CNTNAP5):​c.1358C>T​(p.Ser453Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0408 in 1,613,644 control chromosomes in the GnomAD database, including 1,554 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.034 ( 130 hom., cov: 32)
Exomes 𝑓: 0.041 ( 1424 hom. )

Consequence

CNTNAP5
NM_001367498.1 missense

Scores

1
7
10

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.85
Variant links:
Genes affected
CNTNAP5 (HGNC:18748): (contactin associated protein family member 5) This gene product belongs to the neurexin family, members of which function in the vertebrate nervous system as cell adhesion molecules and receptors. This protein, like other neurexin proteins, contains epidermal growth factor repeats and laminin G domains. In addition, it includes an F5/8 type C domain, discoidin/neuropilin- and fibrinogen-like domains, and thrombospondin N-terminal-like domains. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0045080483).
BP6
Variant 2-124524333-C-T is Benign according to our data. Variant chr2-124524333-C-T is described in ClinVar as [Benign]. Clinvar id is 3056463.Status of the report is no_assertion_criteria_provided, 0 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0342 (5201/152174) while in subpopulation NFE AF= 0.0458 (3113/68006). AF 95% confidence interval is 0.0444. There are 130 homozygotes in gnomad4. There are 2715 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 130 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CNTNAP5NM_001367498.1 linkuse as main transcriptc.1358C>T p.Ser453Leu missense_variant 9/24 ENST00000682447.1
CNTNAP5NM_130773.4 linkuse as main transcriptc.1355C>T p.Ser452Leu missense_variant 9/24
CNTNAP5XM_017003316.2 linkuse as main transcriptc.1358C>T p.Ser453Leu missense_variant 9/23

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CNTNAP5ENST00000682447.1 linkuse as main transcriptc.1358C>T p.Ser453Leu missense_variant 9/24 NM_001367498.1 A1
CNTNAP5ENST00000431078.1 linkuse as main transcriptc.1355C>T p.Ser452Leu missense_variant 9/241 P4

Frequencies

GnomAD3 genomes
AF:
0.0342
AC:
5206
AN:
152058
Hom.:
130
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00667
Gnomad AMI
AF:
0.0779
Gnomad AMR
AF:
0.0289
Gnomad ASJ
AF:
0.0464
Gnomad EAS
AF:
0.000772
Gnomad SAS
AF:
0.0149
Gnomad FIN
AF:
0.0903
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.0458
Gnomad OTH
AF:
0.0483
GnomAD3 exomes
AF:
0.0360
AC:
8958
AN:
248590
Hom.:
250
AF XY:
0.0364
AC XY:
4910
AN XY:
134826
show subpopulations
Gnomad AFR exome
AF:
0.00484
Gnomad AMR exome
AF:
0.0186
Gnomad ASJ exome
AF:
0.0504
Gnomad EAS exome
AF:
0.000279
Gnomad SAS exome
AF:
0.0153
Gnomad FIN exome
AF:
0.0841
Gnomad NFE exome
AF:
0.0466
Gnomad OTH exome
AF:
0.0341
GnomAD4 exome
AF:
0.0415
AC:
60635
AN:
1461470
Hom.:
1424
Cov.:
31
AF XY:
0.0413
AC XY:
30058
AN XY:
727016
show subpopulations
Gnomad4 AFR exome
AF:
0.00663
Gnomad4 AMR exome
AF:
0.0199
Gnomad4 ASJ exome
AF:
0.0487
Gnomad4 EAS exome
AF:
0.000227
Gnomad4 SAS exome
AF:
0.0164
Gnomad4 FIN exome
AF:
0.0810
Gnomad4 NFE exome
AF:
0.0450
Gnomad4 OTH exome
AF:
0.0372
GnomAD4 genome
AF:
0.0342
AC:
5201
AN:
152174
Hom.:
130
Cov.:
32
AF XY:
0.0365
AC XY:
2715
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.00667
Gnomad4 AMR
AF:
0.0289
Gnomad4 ASJ
AF:
0.0464
Gnomad4 EAS
AF:
0.000774
Gnomad4 SAS
AF:
0.0143
Gnomad4 FIN
AF:
0.0903
Gnomad4 NFE
AF:
0.0458
Gnomad4 OTH
AF:
0.0473
Alfa
AF:
0.0423
Hom.:
337
Bravo
AF:
0.0285
TwinsUK
AF:
0.0437
AC:
162
ALSPAC
AF:
0.0405
AC:
156
ESP6500AA
AF:
0.00553
AC:
23
ESP6500EA
AF:
0.0509
AC:
429
ExAC
AF:
0.0339
AC:
4107
Asia WGS
AF:
0.00808
AC:
28
AN:
3478
EpiCase
AF:
0.0500
EpiControl
AF:
0.0503

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

CNTNAP5-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesMay 02, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.083
BayesDel_addAF
Benign
-0.39
T
BayesDel_noAF
Benign
-0.30
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.49
T
Eigen
Benign
-0.049
Eigen_PC
Benign
0.070
FATHMM_MKL
Uncertain
0.87
D
LIST_S2
Uncertain
0.90
D
MetaRNN
Benign
0.0045
T
MetaSVM
Benign
-0.70
T
MutationAssessor
Uncertain
2.6
M
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.51
T
PROVEAN
Pathogenic
-4.8
D
REVEL
Benign
0.28
Sift
Benign
0.048
D
Sift4G
Uncertain
0.057
T
Polyphen
0.011
B
Vest4
0.090
MPC
0.077
ClinPred
0.041
T
GERP RS
6.0
Varity_R
0.49
gMVP
0.77

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17727261; hg19: chr2-125281910; COSMIC: COSV70497527; API