GeneBe

rs58879635

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_000088.4(COL1A1):​c.*1020_*1026delTTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000736 in 122,228 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 0.000041 ( 0 hom., cov: 26)
Exomes 𝑓: 0.00012 ( 0 hom. )

Consequence

COL1A1
NM_000088.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.77
Variant links:
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 Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAdExome4 at 6 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
COL1A1NM_000088.4 linkc.*1020_*1026delTTTTTTT 3_prime_UTR_variant Exon 51 of 51 ENST00000225964.10 NP_000079.2 P02452
COL1A1XM_011524341.2 linkc.*1020_*1026delTTTTTTT 3_prime_UTR_variant Exon 48 of 48 XP_011522643.1
COL1A1XM_005257058.5 linkc.*1020_*1026delTTTTTTT 3_prime_UTR_variant Exon 49 of 49 XP_005257115.2
COL1A1XM_005257059.5 linkc.*1020_*1026delTTTTTTT 3_prime_UTR_variant Exon 38 of 38 XP_005257116.2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COL1A1ENST00000225964 linkc.*1020_*1026delTTTTTTT 3_prime_UTR_variant Exon 51 of 51 1 NM_000088.4 ENSP00000225964.6 P02452

Frequencies

GnomAD3 genomes
AF:
0.0000410
AC:
3
AN:
73110
Hom.:
0
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.000143
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000122
AC:
6
AN:
49118
Hom.:
0
AF XY:
0.0000439
AC XY:
1
AN XY:
22784
show subpopulations
Gnomad4 AFR exome
AF:
0.000454
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.000317
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000134
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000410
AC:
3
AN:
73110
Hom.:
0
Cov.:
26
AF XY:
0.0000863
AC XY:
3
AN XY:
34744
show subpopulations
Gnomad4 AFR
AF:
0.000143
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs58879635; hg19: chr17-48261836; API