21-46125500-TTCGTCA-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PM4PP3PP5
The NM_001849.4(COL6A2):c.1856_1861del(p.Val619_Ile620del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,680 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. F618F) has been classified as Likely benign.
Frequency
Consequence
NM_001849.4 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A2 | NM_001849.4 | c.1856_1861del | p.Val619_Ile620del | inframe_deletion | 25/28 | ENST00000300527.9 | |
COL6A2 | NM_058174.3 | c.1856_1861del | p.Val619_Ile620del | inframe_deletion | 25/28 | ENST00000397763.6 | |
COL6A2 | NM_058175.3 | c.1856_1861del | p.Val619_Ile620del | inframe_deletion | 25/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A2 | ENST00000300527.9 | c.1856_1861del | p.Val619_Ile620del | inframe_deletion | 25/28 | 1 | NM_001849.4 | P1 | |
COL6A2 | ENST00000397763.6 | c.1856_1861del | p.Val619_Ile620del | inframe_deletion | 25/28 | 5 | NM_058174.3 | ||
COL6A2 | ENST00000409416.6 | c.1856_1861del | p.Val619_Ile620del | inframe_deletion | 24/27 | 5 | |||
COL6A2 | ENST00000413758.1 | c.527_532del | p.Val176_Ile177del | inframe_deletion | 10/11 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460680Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 726642
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Ullrich congenital muscular dystrophy 1B Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 22, 2010 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at