rs375643696

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS1

The NM_001201380.3(CNTNAP3B):​c.1844del​(p.Leu615ArgfsTer10) variant causes a frameshift change. The variant allele was found at a frequency of 0.00348 in 151,468 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (β˜…). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0035 ( 0 hom., cov: 48)
Exomes 𝑓: 0.0047 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

CNTNAP3B
NM_001201380.3 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.32
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6
Variant 9-41960804-CA-C is Benign according to our data. Variant chr9-41960804-CA-C is described in ClinVar as [Benign]. Clinvar id is 402551.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00348 (527/151468) while in subpopulation SAS AF= 0.0425 (193/4536). AF 95% confidence interval is 0.0376. There are 0 homozygotes in gnomad4. There are 319 alleles in male gnomad4 subpopulation. Median coverage is 48. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CNTNAP3BNM_001201380.3 linkuse as main transcriptc.1844del p.Leu615ArgfsTer10 frameshift_variant 12/24 ENST00000377561.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CNTNAP3BENST00000377561.7 linkuse as main transcriptc.1844del p.Leu615ArgfsTer10 frameshift_variant 12/241 NM_001201380.3 P1Q96NU0-1

Frequencies

GnomAD3 genomes
AF:
0.00350
AC:
530
AN:
151348
Hom.:
0
Cov.:
48
show subpopulations
Gnomad AFR
AF:
0.000434
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00243
Gnomad ASJ
AF:
0.0286
Gnomad EAS
AF:
0.00568
Gnomad SAS
AF:
0.0432
Gnomad FIN
AF:
0.000188
Gnomad MID
AF:
0.00318
Gnomad NFE
AF:
0.00210
Gnomad OTH
AF:
0.00434
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00466
AC:
6718
AN:
1442056
Hom.:
0
Cov.:
35
AF XY:
0.00577
AC XY:
4133
AN XY:
715978
show subpopulations
Gnomad4 AFR exome
AF:
0.000577
Gnomad4 AMR exome
AF:
0.00201
Gnomad4 ASJ exome
AF:
0.0229
Gnomad4 EAS exome
AF:
0.0131
Gnomad4 SAS exome
AF:
0.0387
Gnomad4 FIN exome
AF:
0.000226
Gnomad4 NFE exome
AF:
0.00179
Gnomad4 OTH exome
AF:
0.00615
GnomAD4 genome
AF:
0.00348
AC:
527
AN:
151468
Hom.:
0
Cov.:
48
AF XY:
0.00431
AC XY:
319
AN XY:
73968
show subpopulations
Gnomad4 AFR
AF:
0.000433
Gnomad4 AMR
AF:
0.00243
Gnomad4 ASJ
AF:
0.0286
Gnomad4 EAS
AF:
0.00569
Gnomad4 SAS
AF:
0.0425
Gnomad4 FIN
AF:
0.000188
Gnomad4 NFE
AF:
0.00210
Gnomad4 OTH
AF:
0.00429
Alfa
AF:
0.00645
Hom.:
2

ClinVar

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

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineMar 28, 2016Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs375643696; hg19: chr9-65595156; API