rs1537504

Variant summary

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

The NM_001855.5(COL15A1):​c.3837+193G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151,996 control chromosomes in the GnomAD database, including 6,452 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 0.28 ( 6452 hom., cov: 31)

Consequence

COL15A1
NM_001855.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.162
Variant links:
Genes affected
COL15A1 (HGNC:2192): (collagen type XV alpha 1 chain) This gene encodes the alpha chain of type XV collagen, a member of the FACIT collagen family (fibril-associated collagens with interrupted helices). Type XV collagen has a wide tissue distribution but the strongest expression is localized to basement membrane zones so it may function to adhere basement membranes to underlying connective tissue stroma. The proteolytically produced C-terminal fragment of type XV collagen is restin, a potentially antiangiogenic protein that is closely related to endostatin. Mouse studies have shown that collagen XV deficiency is associated with muscle and microvessel deterioration. [provided by RefSeq, May 2013]

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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=-0.7).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
COL15A1NM_001855.5 linkuse as main transcriptc.3837+193G>A intron_variant ENST00000375001.8 NP_001846.3 P39059B3KTP7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
COL15A1ENST00000375001.8 linkuse as main transcriptc.3837+193G>A intron_variant 1 NM_001855.5 ENSP00000364140.3 P39059
COL15A1ENST00000610452.1 linkuse as main transcriptc.3795+193G>A intron_variant 5 A0A087X0K0

Frequencies

GnomAD3 genomes
AF:
0.278
AC:
42259
AN:
151878
Hom.:
6447
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.321
Gnomad AMI
AF:
0.196
Gnomad AMR
AF:
0.321
Gnomad ASJ
AF:
0.237
Gnomad EAS
AF:
0.601
Gnomad SAS
AF:
0.450
Gnomad FIN
AF:
0.171
Gnomad MID
AF:
0.263
Gnomad NFE
AF:
0.226
Gnomad OTH
AF:
0.298
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.278
AC:
42284
AN:
151996
Hom.:
6452
Cov.:
31
AF XY:
0.280
AC XY:
20795
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.320
Gnomad4 AMR
AF:
0.320
Gnomad4 ASJ
AF:
0.237
Gnomad4 EAS
AF:
0.601
Gnomad4 SAS
AF:
0.451
Gnomad4 FIN
AF:
0.171
Gnomad4 NFE
AF:
0.226
Gnomad4 OTH
AF:
0.298
Alfa
AF:
0.247
Hom.:
2374
Bravo
AF:
0.291
Asia WGS
AF:
0.505
AC:
1753
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.70
CADD
Benign
5.6
DANN
Benign
0.77

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: rs1537504; hg19: chr9-101829542; API