17-50184475-CAAAAAAA-CAAAA
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_000088.4(COL1A1):c.*1024_*1026delTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00766 in 120,632 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00015 ( 0 hom., cov: 26)
Exomes 𝑓: 0.019 ( 0 hom. )
Consequence
COL1A1
NM_000088.4 3_prime_UTR
NM_000088.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.77
Genes affected
COL1A1 (HGNC:2197): (collagen type I alpha 1 chain) This gene encodes the pro-alpha1 chains of type I collagen whose triple helix comprises two alpha1 chains and one alpha2 chain. Type I is a fibril-forming collagen found in most connective tissues and is abundant in bone, cornea, dermis and tendon. Mutations in this gene are associated with osteogenesis imperfecta types I-IV, Ehlers-Danlos syndrome type VIIA, Ehlers-Danlos syndrome Classical type, Caffey Disease and idiopathic osteoporosis. Reciprocal translocations between chromosomes 17 and 22, where this gene and the gene for platelet-derived growth factor beta are located, are associated with a particular type of skin tumor called dermatofibrosarcoma protuberans, resulting from unregulated expression of the growth factor. Two transcripts, resulting from the use of alternate polyadenylation signals, have been identified for this gene. [provided by R. Dalgleish, Feb 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0192 (913/47538) while in subpopulation MID AF= 0.0379 (11/290). AF 95% confidence interval is 0.0217. There are 0 homozygotes in gnomad4_exome. There are 430 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
BS2
High AC in GnomAd4 at 11 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| COL1A1 | NM_000088.4 | c.*1024_*1026delTTT | 3_prime_UTR_variant | Exon 51 of 51 | ENST00000225964.10 | NP_000079.2 | ||
| COL1A1 | XM_011524341.2 | c.*1024_*1026delTTT | 3_prime_UTR_variant | Exon 48 of 48 | XP_011522643.1 | |||
| COL1A1 | XM_005257058.5 | c.*1024_*1026delTTT | 3_prime_UTR_variant | Exon 49 of 49 | XP_005257115.2 | |||
| COL1A1 | XM_005257059.5 | c.*1024_*1026delTTT | 3_prime_UTR_variant | Exon 38 of 38 | XP_005257116.2 |
Ensembl
Frequencies
GnomAD3 genomes 0.000150 AC: 11AN: 73094Hom.: 0 Cov.: 26
GnomAD3 genomes
AF:
AC:
11
AN:
73094
Hom.:
Cov.:
26
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0192 AC: 913AN: 47538Hom.: 0 AF XY: 0.0195 AC XY: 430AN XY: 22010
GnomAD4 exome
AF:
AC:
913
AN:
47538
Hom.:
AF XY:
AC XY:
430
AN XY:
22010
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome 0.000150 AC: 11AN: 73094Hom.: 0 Cov.: 26 AF XY: 0.000201 AC XY: 7AN XY: 34754
GnomAD4 genome
AF:
AC:
11
AN:
73094
Hom.:
Cov.:
26
AF XY:
AC XY:
7
AN XY:
34754
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at