Genetic Variant CADM1:c.*3118C>T (chr11-115173356-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001301043.2(CADM1):c.*3118C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,158 control chromosomes in the GnomAD database, including 15,012 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.43 ( 14986 hom., cov: 33)

Exomes 𝑓: 0.60 ( 26 hom. )

Consequence

CADM1
NM_001301043.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.918

Publications

5 publications found

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 Gene-Disease associations (from GenCC):

autism spectrum disorder
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

CADM1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CADM1	NM_001301043.2	MANE Select	c.*3118C>T	3_prime_UTR	Exon 12 of 12	NP_001287972.1
CADM1	NM_001301044.2		c.*3118C>T	3_prime_UTR	Exon 11 of 11	NP_001287973.1
CADM1	NM_001301045.2		c.*3118C>T	3_prime_UTR	Exon 11 of 11	NP_001287974.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CADM1	ENST00000331581.11	TSL:1 MANE Select	c.*3118C>T	3_prime_UTR	Exon 12 of 12	ENSP00000329797.6
CADM1	ENST00000452722.7	TSL:1	c.*3118C>T	3_prime_UTR	Exon 10 of 10	ENSP00000395359.2
CADM1	ENST00000537140.5	TSL:1	n.1256-3730C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.425

AC:

64628

AN:

151922

Hom.:

14984

Cov.:

show subpopulations

Gnomad AFR

AF:

0.266

Gnomad AMI

AF:

0.533

Gnomad AMR

AF:

0.395

Gnomad ASJ

AF:

0.488

Gnomad EAS

AF:

0.198

Gnomad SAS

AF:

0.407

Gnomad FIN

AF:

0.499

Gnomad MID

AF:

0.379

Gnomad NFE

AF:

0.531

Gnomad OTH

AF:

0.442

GnomAD4 exome

AF:

0.602

AC:

AN:

118

Hom.:

Cov.:

AF XY:

0.625

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.700

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.652

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

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

GnomAD4 genome

AF:

0.425

AC:

64638

AN:

152040

Hom.:

14986

Cov.:

AF XY:

0.424

AC XY:

31484

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.266

AC:

11045

AN:

41500

American (AMR)

AF:

0.395

AC:

6037

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.488

AC:

1691

AN:

3468

East Asian (EAS)

AF:

0.198

AC:

1020

AN:

5152

South Asian (SAS)

AF:

0.407

AC:

1958

AN:

4816

European-Finnish (FIN)

AF:

0.499

AC:

5282

AN:

10588

Middle Eastern (MID)

AF:

0.384

AC:

112

AN:

292

European-Non Finnish (NFE)

AF:

0.531

AC:

36086

AN:

67932

Other (OTH)

AF:

0.438

AC:

922

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1811

3622

5433

7244

9055

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

612

1224

1836

2448

3060

<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:

0.481

Hom.:

6922

Bravo

AF:

0.410

Asia WGS

AF:

0.274

AC:

955

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.2

(source)

DANN

Benign

0.88

PhyloP100

0.92

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over