chr6-56077530-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_030820.4(COL21A1):āc.1856A>Cā(p.Lys619Thr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000126 in 1,423,704 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 Uncertain significance (ā ).
Frequency
Consequence
NM_030820.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL21A1 | NM_030820.4 | c.1856A>C | p.Lys619Thr | missense_variant, splice_region_variant | 18/30 | ENST00000244728.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL21A1 | ENST00000244728.10 | c.1856A>C | p.Lys619Thr | missense_variant, splice_region_variant | 18/30 | 1 | NM_030820.4 | A1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000187 AC: 4AN: 214294Hom.: 0 AF XY: 0.00000862 AC XY: 1AN XY: 116046
GnomAD4 exome AF: 0.0000126 AC: 18AN: 1423704Hom.: 0 Cov.: 27 AF XY: 0.0000170 AC XY: 12AN XY: 706882
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2022 | The c.1856A>C (p.K619T) alteration is located in exon 18 (coding exon 17) of the COL21A1 gene. This alteration results from a A to C substitution at nucleotide position 1856, causing the lysine (K) at amino acid position 619 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at