chr6-56124072-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_030820.4(COL21A1):āc.1748C>Gā(p.Pro583Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0138 in 1,515,634 control chromosomes in the GnomAD database, including 170 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P583S) has been classified as Uncertain significance.
Frequency
Consequence
NM_030820.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL21A1 | NM_030820.4 | c.1748C>G | p.Pro583Arg | missense_variant | 16/30 | ENST00000244728.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL21A1 | ENST00000244728.10 | c.1748C>G | p.Pro583Arg | missense_variant | 16/30 | 1 | NM_030820.4 | A1 | |
COL21A1 | ENST00000370819.5 | c.1739C>G | p.Pro580Arg | missense_variant | 15/29 | 1 | P4 | ||
COL21A1 | ENST00000488912.5 | c.140C>G | p.Pro47Arg | missense_variant, NMD_transcript_variant | 3/18 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0104 AC: 1540AN: 148786Hom.: 17 Cov.: 32
GnomAD3 exomes AF: 0.00882 AC: 1168AN: 132470Hom.: 10 AF XY: 0.00863 AC XY: 602AN XY: 69748
GnomAD4 exome AF: 0.0142 AC: 19402AN: 1366768Hom.: 153 Cov.: 31 AF XY: 0.0141 AC XY: 9464AN XY: 673458
GnomAD4 genome AF: 0.0103 AC: 1538AN: 148866Hom.: 17 Cov.: 32 AF XY: 0.00986 AC XY: 715AN XY: 72490
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 17, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at