11-115181915-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001301043.2(CADM1):​c.1166-3140T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,188 control chromosomes in the GnomAD database, including 3,789 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 0.21 ( 3789 hom., cov: 32)

Consequence

CADM1
NM_001301043.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.33
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CADM1NM_001301043.2 linkuse as main transcriptc.1166-3140T>G intron_variant ENST00000331581.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CADM1ENST00000331581.11 linkuse as main transcriptc.1166-3140T>G intron_variant 1 NM_001301043.2 P4Q9BY67-3

Frequencies

GnomAD3 genomes
AF:
0.208
AC:
31631
AN:
152070
Hom.:
3784
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.105
Gnomad AMI
AF:
0.0714
Gnomad AMR
AF:
0.287
Gnomad ASJ
AF:
0.171
Gnomad EAS
AF:
0.142
Gnomad SAS
AF:
0.322
Gnomad FIN
AF:
0.272
Gnomad MID
AF:
0.228
Gnomad NFE
AF:
0.244
Gnomad OTH
AF:
0.196
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.208
AC:
31642
AN:
152188
Hom.:
3789
Cov.:
32
AF XY:
0.211
AC XY:
15681
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.105
Gnomad4 AMR
AF:
0.287
Gnomad4 ASJ
AF:
0.171
Gnomad4 EAS
AF:
0.142
Gnomad4 SAS
AF:
0.323
Gnomad4 FIN
AF:
0.272
Gnomad4 NFE
AF:
0.244
Gnomad4 OTH
AF:
0.193
Alfa
AF:
0.212
Hom.:
439
Bravo
AF:
0.202
Asia WGS
AF:
0.230
AC:
798
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.13
DANN
Benign
0.44

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11215400; hg19: chr11-115052635; API