GeneBe

11-115209591-ATGGTGGTGGTGGTGGTGGTGG-ATGGTGGTGGTGGTGGTGGTGGTGGTGG

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2

The NM_001301043.2(CADM1):​c.1055_1060dupCCACCA​(p.Thr352_Thr353dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000465 in 924,976 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00032 ( 1 hom. )

Consequence

CADM1
NM_001301043.2 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.07
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_001301043.2
BS2
High AC in GnomAd4 at 178 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CADM1NM_001301043.2 linkc.1055_1060dupCCACCA p.Thr352_Thr353dup conservative_inframe_insertion Exon 8 of 12 ENST00000331581.11 NP_001287972.1 Q9BY67-3X5D7A8A0A4Z1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CADM1ENST00000331581.11 linkc.1055_1060dupCCACCA p.Thr352_Thr353dup conservative_inframe_insertion Exon 8 of 12 1 NM_001301043.2 ENSP00000329797.6 Q9BY67-3

Frequencies

GnomAD3 genomes
AF:
0.00129
AC:
179
AN:
139034
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00432
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000286
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000536
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000626
Gnomad OTH
AF:
0.00102
GnomAD3 exomes
AF:
0.000296
AC:
63
AN:
212678
Hom.:
0
AF XY:
0.000225
AC XY:
26
AN XY:
115448
show subpopulations
Gnomad AFR exome
AF:
0.00350
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000204
Gnomad SAS exome
AF:
0.000231
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000620
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000321
AC:
252
AN:
785818
Hom.:
1
Cov.:
33
AF XY:
0.000298
AC XY:
122
AN XY:
409300
show subpopulations
Gnomad4 AFR exome
AF:
0.00817
Gnomad4 AMR exome
AF:
0.000150
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000783
Gnomad4 SAS exome
AF:
0.000207
Gnomad4 FIN exome
AF:
0.0000248
Gnomad4 NFE exome
AF:
0.000102
Gnomad4 OTH exome
AF:
0.000294
GnomAD4 genome
AF:
0.00128
AC:
178
AN:
139158
Hom.:
0
Cov.:
32
AF XY:
0.00131
AC XY:
88
AN XY:
67384
show subpopulations
Gnomad4 AFR
AF:
0.00431
Gnomad4 AMR
AF:
0.000286
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000267
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000626
Gnomad4 OTH
AF:
0.00101

ClinVar

Not reported in ClinVar

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: rs747352768; hg19: chr11-115080311; API