NM_152750.5:c.2353+605C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_152750.5(CDHR3):​c.2353+605C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0151 in 152,232 control chromosomes in the GnomAD database, including 25 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 0.015 ( 25 hom., cov: 33)

Consequence

CDHR3
NM_152750.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11

Publications

1 publications found
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]

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=-0.54).
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0151 (2302/152232) while in subpopulation AFR AF = 0.0218 (907/41540). AF 95% confidence interval is 0.0207. There are 25 homozygotes in GnomAd4. There are 1100 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 25 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CDHR3NM_152750.5 linkc.2353+605C>T intron_variant Intron 18 of 18 ENST00000317716.14 NP_689963.2 Q6ZTQ4-1
CDHR3NM_001301161.2 linkc.2089+605C>T intron_variant Intron 17 of 17 NP_001288090.1 Q6ZTQ4E7EQG5B7Z8X2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CDHR3ENST00000317716.14 linkc.2353+605C>T intron_variant Intron 18 of 18 1 NM_152750.5 ENSP00000325954.9 Q6ZTQ4-1

Frequencies

GnomAD3 genomes
AF:
0.0151
AC:
2295
AN:
152114
Hom.:
25
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0217
Gnomad AMI
AF:
0.00548
Gnomad AMR
AF:
0.00870
Gnomad ASJ
AF:
0.0121
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.00748
Gnomad FIN
AF:
0.0169
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0141
Gnomad OTH
AF:
0.0167
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0151
AC:
2302
AN:
152232
Hom.:
25
Cov.:
33
AF XY:
0.0148
AC XY:
1100
AN XY:
74410
show subpopulations
African (AFR)
AF:
0.0218
AC:
907
AN:
41540
American (AMR)
AF:
0.00869
AC:
133
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
0.0121
AC:
42
AN:
3472
East Asian (EAS)
AF:
0.000387
AC:
2
AN:
5174
South Asian (SAS)
AF:
0.00748
AC:
36
AN:
4810
European-Finnish (FIN)
AF:
0.0169
AC:
179
AN:
10598
Middle Eastern (MID)
AF:
0.00340
AC:
1
AN:
294
European-Non Finnish (NFE)
AF:
0.0141
AC:
961
AN:
68018
Other (OTH)
AF:
0.0170
AC:
36
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
110
220
330
440
550
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
26
52
78
104
130
<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:
0.0135
Hom.:
6
Bravo
AF:
0.0149
Asia WGS
AF:
0.0160
AC:
55
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
9.3
DANN
Benign
0.80
PhyloP100
-1.1
Mutation Taster
=100/0
polymorphism

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

Other links and lift over

dbSNP: rs17152486; hg19: chr7-105671891; API