11-115209591-ATGGTGGTGGTGGTGGTGGTGG-ATGGTGG
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP3BS2
The NM_001301043.2(CADM1):c.1046_1060delCCACCACCACCACCA(p.Thr349_Thr353del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000238 in 925,008 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000029 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
CADM1
NM_001301043.2 disruptive_inframe_deletion
NM_001301043.2 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.96
Publications
3 publications found
Genes affected
CADM1 (HGNC:5951): (cell adhesion molecule 1) Enables signaling receptor binding activity. Involved in several processes, including cell recognition; positive regulation of cytokine production; and susceptibility to natural killer cell mediated cytotoxicity. Located in plasma membrane. Implicated in breast carcinoma and prostate cancer. Biomarker of cervix uteri carcinoma in situ. [provided by Alliance of Genome Resources, Apr 2022]
CADM1 Gene-Disease associations (from GenCC):
- autism spectrum disorderInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001301043.2
BS2
High AC in GnomAdExome4 at 18 AD gene.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001301043.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CADM1 | MANE Select | c.1046_1060delCCACCACCACCACCA | p.Thr349_Thr353del | disruptive_inframe_deletion | Exon 8 of 12 | NP_001287972.1 | Q9BY67-3 | ||
| CADM1 | c.1046_1060delCCACCACCACCACCA | p.Thr349_Thr353del | disruptive_inframe_deletion | Exon 8 of 11 | NP_001287973.1 | X5DQR8 | |||
| CADM1 | c.1046_1060delCCACCACCACCACCA | p.Thr349_Thr353del | disruptive_inframe_deletion | Exon 8 of 10 | NP_055148.3 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CADM1 | TSL:1 MANE Select | c.1046_1060delCCACCACCACCACCA | p.Thr349_Thr353del | disruptive_inframe_deletion | Exon 8 of 12 | ENSP00000329797.6 | Q9BY67-3 | ||
| CADM1 | TSL:1 | c.1046_1060delCCACCACCACCACCA | p.Thr349_Thr353del | disruptive_inframe_deletion | Exon 8 of 11 | ENSP00000439817.1 | Q9BY67-4 | ||
| CADM1 | TSL:1 | c.1046_1060delCCACCACCACCACCA | p.Thr349_Thr353del | disruptive_inframe_deletion | Exon 8 of 10 | ENSP00000395359.2 | Q9BY67-1 |
Frequencies
GnomAD3 genomes 0.0000288 AC: 4AN: 139040Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
4
AN:
139040
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000229 AC: 18AN: 785844Hom.: 0 AF XY: 0.0000195 AC XY: 8AN XY: 409312 show subpopulations
GnomAD4 exome
AF:
AC:
18
AN:
785844
Hom.:
AF XY:
AC XY:
8
AN XY:
409312
show subpopulations
African (AFR)
AF:
AC:
1
AN:
20070
American (AMR)
AF:
AC:
0
AN:
39932
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
17920
East Asian (EAS)
AF:
AC:
1
AN:
25552
South Asian (SAS)
AF:
AC:
0
AN:
72318
European-Finnish (FIN)
AF:
AC:
1
AN:
40370
Middle Eastern (MID)
AF:
AC:
0
AN:
3922
European-Non Finnish (NFE)
AF:
AC:
15
AN:
531722
Other (OTH)
AF:
AC:
0
AN:
34038
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
0
1
3
4
6
7
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.0000287 AC: 4AN: 139164Hom.: 0 Cov.: 32 AF XY: 0.0000594 AC XY: 4AN XY: 67386 show subpopulations
GnomAD4 genome
AF:
AC:
4
AN:
139164
Hom.:
Cov.:
32
AF XY:
AC XY:
4
AN XY:
67386
show subpopulations
African (AFR)
AF:
AC:
3
AN:
38730
American (AMR)
AF:
AC:
0
AN:
14006
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3274
East Asian (EAS)
AF:
AC:
1
AN:
4006
South Asian (SAS)
AF:
AC:
0
AN:
3746
European-Finnish (FIN)
AF:
AC:
0
AN:
8424
Middle Eastern (MID)
AF:
AC:
0
AN:
282
European-Non Finnish (NFE)
AF:
AC:
0
AN:
63854
Other (OTH)
AF:
AC:
0
AN:
1988
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.538
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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