rs17168526
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001037763.3(COL28A1):āc.240A>Gā(p.Gln80=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00426 in 1,605,212 control chromosomes in the GnomAD database, including 243 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.022 ( 146 hom., cov: 32)
Exomes š: 0.0024 ( 97 hom. )
Consequence
COL28A1
NM_001037763.3 synonymous
NM_001037763.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.93
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BP6
?
Variant 7-7531789-T-C is Benign according to our data. Variant chr7-7531789-T-C is described in ClinVar as [Benign]. Clinvar id is 776205.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.93 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0739 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL28A1 | NM_001037763.3 | c.240A>G | p.Gln80= | synonymous_variant | 3/35 | ENST00000399429.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL28A1 | ENST00000399429.8 | c.240A>G | p.Gln80= | synonymous_variant | 3/35 | 1 | NM_001037763.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0219 AC: 3329AN: 152186Hom.: 147 Cov.: 32
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GnomAD3 exomes AF: 0.00573 AC: 1426AN: 248946Hom.: 45 AF XY: 0.00455 AC XY: 614AN XY: 135046
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GnomAD4 exome AF: 0.00240 AC: 3494AN: 1452906Hom.: 97 Cov.: 27 AF XY: 0.00211 AC XY: 1524AN XY: 723584
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GnomAD4 genome ? AF: 0.0219 AC: 3338AN: 152306Hom.: 146 Cov.: 32 AF XY: 0.0217 AC XY: 1616AN XY: 74498
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 25, 2017 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at