rs374268357
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000225964.10(COL1A1):c.1461+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000978 in 1,564,204 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000225964.10 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL1A1 | NM_000088.4 | c.1461+7G>A | splice_region_variant, intron_variant | ENST00000225964.10 | NP_000079.2 | |||
COL1A1 | XM_005257058.5 | c.1461+7G>A | splice_region_variant, intron_variant | XP_005257115.2 | ||||
COL1A1 | XM_005257059.5 | c.957+1600G>A | intron_variant | XP_005257116.2 | ||||
COL1A1 | XM_011524341.2 | c.1263+7G>A | splice_region_variant, intron_variant | XP_011522643.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL1A1 | ENST00000225964.10 | c.1461+7G>A | splice_region_variant, intron_variant | 1 | NM_000088.4 | ENSP00000225964 | P1 | |||
COL1A1 | ENST00000471344.1 | n.405+7G>A | splice_region_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000513 AC: 78AN: 151968Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000137 AC: 24AN: 174920Hom.: 0 AF XY: 0.0000641 AC XY: 6AN XY: 93662
GnomAD4 exome AF: 0.0000531 AC: 75AN: 1412118Hom.: 0 Cov.: 36 AF XY: 0.0000415 AC XY: 29AN XY: 698334
GnomAD4 genome AF: 0.000513 AC: 78AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.000350 AC XY: 26AN XY: 74368
ClinVar
Submissions by phenotype
COL1A1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 05, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Osteogenesis imperfecta type I Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 04, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at