Genetic Variant CADM1:p.Thr353dup (chr11-115209591-A-ATGG) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -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]

CADM1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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. GnomAdExome4 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 GnomAdExome4. There are 1157 alleles in the male GnomAdExome4 subpopulation. Median coverage is 33. This position FAILED quality control check.

BS2

High AC in GnomAd4 at 610 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CADM1	NM_001301043.2 link	c.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
CADM1	ENST00000331581.11 link	c.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.:

Cov.:

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

GnomAD2 exomes

AF:

0.00270

AC:

574

AN:

212678

AF XY:

0.00252

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 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.:

Cov.:

AF XY:

0.00283

AC XY:

1157

AN XY:

409088

show subpopulations

Gnomad4 AFR exome

AF:

0.0199

AC:

400

AN:

20052

Gnomad4 AMR exome

AF:

0.00358

AC:

143

AN:

39926

Gnomad4 ASJ exome

AF:

0.0000558

AC:

AN:

17920

Gnomad4 EAS exome

AF:

0.0110

AC:

281

AN:

25550

Gnomad4 SAS exome

AF:

0.00348

AC:

252

AN:

72310

Gnomad4 FIN exome

AF:

0.000322

AC:

AN:

40370

Gnomad4 NFE exome

AF:

0.00198

AC:

1050

AN:

531266

Gnomad4 Remaining exome

AF:

0.00453

AC:

154

AN:

34028

Heterozygous variant carriers

108

215

323

430

538

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

104

156

208

260

<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

AF:

0.00438

AC:

610

AN:

139158

Hom.:

Cov.:

AF XY:

0.00421

AC XY:

284

AN XY:

67386

show subpopulations

Gnomad4 AFR

AF:

0.0115

AC:

0.0114898

AN:

0.0114898

Gnomad4 AMR

AF:

0.00200

AC:

0.00199914

AN:

0.00199914

Gnomad4 ASJ

AF:

0.00

AC:

AN:

Gnomad4 EAS

AF:

0.00574

AC:

0.00574426

AN:

0.00574426

Gnomad4 SAS

AF:

0.00374

AC:

0.00373732

AN:

0.00373732

Gnomad4 FIN

AF:

0.000712

AC:

0.00071242

AN:

0.00071242

Gnomad4 NFE

AF:

0.00105

AC:

0.0010493

AN:

0.0010493

Gnomad4 OTH

AF:

0.00201

AC:

0.00201207

AN:

0.00201207

Heterozygous variant carriers

114

142

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000255

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Dec 06, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mutation Taster

=75/25

polymorphism

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over