rs13438712

Variant summary

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

The ENST00000488386.5(CDHR3):​c.-16+24877T>C variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,142 control chromosomes in the GnomAD database, including 7,835 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 0.31 ( 7835 hom., cov: 32)

Consequence

CDHR3
ENST00000488386.5 intron, NMD_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0350
Variant links:
Genes affected
CDHR3 (HGNC:26308): (cadherin related family member 3) Predicted to enable cadherin binding activity and calcium ion binding activity. Predicted to be involved in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules; cell morphogenesis; and cell-cell junction organization. Located in plasma membrane. [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=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CDHR3ENST00000488386.5 linkuse as main transcriptc.-16+24877T>C intron_variant, NMD_transcript_variant 3 ENSP00000419593
CDHR3ENST00000470188.5 linkuse as main transcriptn.438-8883T>C intron_variant, non_coding_transcript_variant 2
CDHR3ENST00000487084.1 linkuse as main transcriptn.463-8093T>C intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.306
AC:
46471
AN:
152024
Hom.:
7833
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.201
Gnomad AMI
AF:
0.334
Gnomad AMR
AF:
0.297
Gnomad ASJ
AF:
0.394
Gnomad EAS
AF:
0.0427
Gnomad SAS
AF:
0.364
Gnomad FIN
AF:
0.391
Gnomad MID
AF:
0.437
Gnomad NFE
AF:
0.368
Gnomad OTH
AF:
0.334
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.306
AC:
46480
AN:
152142
Hom.:
7835
Cov.:
32
AF XY:
0.307
AC XY:
22854
AN XY:
74374
show subpopulations
Gnomad4 AFR
AF:
0.200
Gnomad4 AMR
AF:
0.296
Gnomad4 ASJ
AF:
0.394
Gnomad4 EAS
AF:
0.0430
Gnomad4 SAS
AF:
0.365
Gnomad4 FIN
AF:
0.391
Gnomad4 NFE
AF:
0.368
Gnomad4 OTH
AF:
0.330
Alfa
AF:
0.357
Hom.:
19839
Bravo
AF:
0.293
Asia WGS
AF:
0.185
AC:
646
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
4.1
DANN
Benign
0.66

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: rs13438712; hg19: chr7-105542580; API