GeneBe

NM_173465.4:c.362-74755G>A

Variant names:

Variant summary

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

The NM_173465.4(COL23A1):​c.362-74755G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,028 control chromosomes in the GnomAD database, including 3,915 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 ( 3915 hom., cov: 32)

Consequence

COL23A1
NM_173465.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.244

Publications

3 publications found
Variant links:
Genes affected
COL23A1 (HGNC:22990): (collagen type XXIII alpha 1 chain) COL23A1 is a member of the transmembrane collagens, a subfamily of the nonfibrillar collagens that contain a single pass hydrophobic transmembrane domain (Banyard et al., 2003 [PubMed 12644459]).[supplied by OMIM, Mar 2008]

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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
COL23A1NM_173465.4 linkc.362-74755G>A intron_variant Intron 2 of 28 ENST00000390654.8 NP_775736.2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COL23A1ENST00000390654.8 linkc.362-74755G>A intron_variant Intron 2 of 28 5 NM_173465.4 ENSP00000375069.3

Frequencies

GnomAD3 genomes
AF:
0.209
AC:
31759
AN:
151910
Hom.:
3903
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.326
Gnomad AMI
AF:
0.107
Gnomad AMR
AF:
0.166
Gnomad ASJ
AF:
0.182
Gnomad EAS
AF:
0.415
Gnomad SAS
AF:
0.295
Gnomad FIN
AF:
0.166
Gnomad MID
AF:
0.193
Gnomad NFE
AF:
0.135
Gnomad OTH
AF:
0.204
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.209
AC:
31818
AN:
152028
Hom.:
3915
Cov.:
32
AF XY:
0.213
AC XY:
15814
AN XY:
74286
show subpopulations
African (AFR)
AF:
0.326
AC:
13532
AN:
41452
American (AMR)
AF:
0.167
AC:
2555
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.182
AC:
632
AN:
3468
East Asian (EAS)
AF:
0.415
AC:
2130
AN:
5128
South Asian (SAS)
AF:
0.295
AC:
1423
AN:
4818
European-Finnish (FIN)
AF:
0.166
AC:
1754
AN:
10572
Middle Eastern (MID)
AF:
0.207
AC:
61
AN:
294
European-Non Finnish (NFE)
AF:
0.135
AC:
9205
AN:
67978
Other (OTH)
AF:
0.202
AC:
428
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1232
2464
3695
4927
6159
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
340
680
1020
1360
1700
<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:
0.181
Hom.:
355
Bravo
AF:
0.215
Asia WGS
AF:
0.320
AC:
1114
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
1.1
DANN
Benign
0.41
PhyloP100
-0.24
Mutation Taster
=100/0
polymorphism (auto)

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: rs2910124; hg19: chr5-177808675; API