GeneBe

rs58548890

Positions:

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_004360.5(CDH1):​c.163+19370_163+19381delCCTTCCTTCCTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00019 ( 1 hom., cov: 0)

Consequence

CDH1
NM_004360.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.460
Variant links:
Genes affected
CDH1 (HGNC:1748): (cadherin 1) This gene encodes a classical cadherin of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature glycoprotein. This calcium-dependent cell-cell adhesion protein is comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Mutations in this gene are correlated with gastric, breast, colorectal, thyroid and ovarian cancer. Loss of function of this gene is thought to contribute to cancer progression by increasing proliferation, invasion, and/or metastasis. The ectodomain of this protein mediates bacterial adhesion to mammalian cells and the cytoplasmic domain is required for internalization. This gene is present in a gene cluster with other members of the cadherin family on chromosome 16. [provided by RefSeq, Nov 2015]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAd4 at 28 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CDH1NM_004360.5 linkuse as main transcriptc.163+19370_163+19381delCCTTCCTTCCTT intron_variant ENST00000261769.10 NP_004351.1 P12830-1A0A0U2ZQU7B3GN61
CDH1NM_001317184.2 linkuse as main transcriptc.163+19370_163+19381delCCTTCCTTCCTT intron_variant NP_001304113.1 P12830-2B3GN61
CDH1NM_001317185.2 linkuse as main transcriptc.-1453+19370_-1453+19381delCCTTCCTTCCTT intron_variant NP_001304114.1 P12830B3GN61Q9UII7
CDH1NM_001317186.2 linkuse as main transcriptc.-1657+19370_-1657+19381delCCTTCCTTCCTT intron_variant NP_001304115.1 P12830B3GN61

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CDH1ENST00000261769.10 linkuse as main transcriptc.163+19370_163+19381delCCTTCCTTCCTT intron_variant 1 NM_004360.5 ENSP00000261769.4 P12830-1
CDH1ENST00000422392.6 linkuse as main transcriptc.163+19370_163+19381delCCTTCCTTCCTT intron_variant 1 ENSP00000414946.2 P12830-2
CDH1ENST00000566612.5 linkuse as main transcriptn.163+19370_163+19381delCCTTCCTTCCTT intron_variant 1 ENSP00000454782.1 H3BNC6
CDH1ENST00000566510.5 linkuse as main transcriptn.163+19370_163+19381delCCTTCCTTCCTT intron_variant 5 ENSP00000458139.1 H3BVI7

Frequencies

GnomAD3 genomes
AF:
0.000169
AC:
25
AN:
147916
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000599
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000685
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.000189
AC:
28
AN:
148034
Hom.:
1
Cov.:
0
AF XY:
0.000223
AC XY:
16
AN XY:
71888
show subpopulations
Gnomad4 AFR
AF:
0.000672
Gnomad4 AMR
AF:
0.0000684
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

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: rs58548890; hg19: chr16-68791670; API