chr7-7370769-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001037763.3(COL28A1):c.3022C>G(p.Leu1008Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,613,698 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001037763.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL28A1 | NM_001037763.3 | c.3022C>G | p.Leu1008Val | missense_variant | 33/35 | ENST00000399429.8 | |
LOC107986764 | XR_002956539.2 | n.442-5792G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL28A1 | ENST00000399429.8 | c.3022C>G | p.Leu1008Val | missense_variant | 33/35 | 1 | NM_001037763.3 | P1 | |
COL28A1 | ENST00000430711.5 | c.73C>G | p.Leu25Val | missense_variant, NMD_transcript_variant | 1/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249434Hom.: 1 AF XY: 0.0000591 AC XY: 8AN XY: 135314
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461610Hom.: 0 Cov.: 30 AF XY: 0.0000481 AC XY: 35AN XY: 727126
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2021 | The c.3022C>G (p.L1008V) alteration is located in exon 33 (coding exon 32) of the COL28A1 gene. This alteration results from a C to G substitution at nucleotide position 3022, causing the leucine (L) at amino acid position 1008 to be replaced by a valine (V). 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