chr11-115209591-A-ATGG

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP3BP6_ModerateBS1BS2

The NM_001301043.2(CADM1):​c.1058_1060dupCCA​(p.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 0.00316 in 924,502 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0044 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0029 ( 2 hom. )

Consequence

CADM1
NM_001301043.2 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

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 Benign. Variant got -11 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_001301043.2
BP6
Variant 11-115209591-A-ATGG is Benign according to our data. Variant chr11-115209591-A-ATGG is described in ClinVar as [Likely_benign]. Clinvar id is 776659.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.00295 (2315/785344) while in subpopulation AFR AF= 0.0199 (400/20052). AF 95% confidence interval is 0.0183. There are 2 homozygotes in gnomad4_exome. There are 1157 alleles in male gnomad4_exome subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 610 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CADM1NM_001301043.2 linkc.1058_1060dupCCA p.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.1058_1060dupCCA p.Thr353dup conservative_inframe_insertion Exon 8 of 12 1 NM_001301043.2 ENSP00000329797.6 Q9BY67-3

Frequencies

GnomAD3 genomes
AF:
0.00437
AC:
607
AN:
139034
Hom.:
3
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0114
Gnomad AMI
AF:
0.0246
Gnomad AMR
AF:
0.00200
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00574
Gnomad SAS
AF:
0.00375
Gnomad FIN
AF:
0.000712
Gnomad MID
AF:
0.00654
Gnomad NFE
AF:
0.00105
Gnomad OTH
AF:
0.00203
GnomAD3 exomes
AF:
0.00270
AC:
574
AN:
212678
Hom.:
0
AF XY:
0.00252
AC XY:
291
AN XY:
115448
show subpopulations
Gnomad AFR exome
AF:
0.0119
Gnomad AMR exome
AF:
0.00387
Gnomad ASJ exome
AF:
0.000113
Gnomad EAS exome
AF:
0.00618
Gnomad SAS exome
AF:
0.00359
Gnomad FIN exome
AF:
0.000263
Gnomad NFE exome
AF:
0.00109
Gnomad OTH exome
AF:
0.000990
GnomAD4 exome
AF:
0.00295
AC:
2315
AN:
785344
Hom.:
2
Cov.:
33
AF XY:
0.00283
AC XY:
1157
AN XY:
409088
show subpopulations
Gnomad4 AFR exome
AF:
0.0199
Gnomad4 AMR exome
AF:
0.00358
Gnomad4 ASJ exome
AF:
0.0000558
Gnomad4 EAS exome
AF:
0.0110
Gnomad4 SAS exome
AF:
0.00348
Gnomad4 FIN exome
AF:
0.000322
Gnomad4 NFE exome
AF:
0.00198
Gnomad4 OTH exome
AF:
0.00453
GnomAD4 genome
AF:
0.00438
AC:
610
AN:
139158
Hom.:
3
Cov.:
32
AF XY:
0.00421
AC XY:
284
AN XY:
67386
show subpopulations
Gnomad4 AFR
AF:
0.0115
Gnomad4 AMR
AF:
0.00200
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00574
Gnomad4 SAS
AF:
0.00374
Gnomad4 FIN
AF:
0.000712
Gnomad4 NFE
AF:
0.00105
Gnomad4 OTH
AF:
0.00201

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 06, 2019- -

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