rs1544926
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173465.4(COL23A1):c.*357C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 233,896 control chromosomes in the GnomAD database, including 19,275 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.36 ( 11517 hom., cov: 33)
Exomes 𝑓: 0.42 ( 7758 hom. )
Consequence
COL23A1
NM_173465.4 3_prime_UTR
NM_173465.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.254
Genes affected
COL23A1 (HGNC:22990): (collagen type XXIII alpha 1 chain) COL23A1 is a member of the transmembrane collagens, a subfamily of the nonfibrillar collagens that contain a single pass hydrophobic transmembrane domain (Banyard et al., 2003 [PubMed 12644459]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL23A1 | NM_173465.4 | c.*357C>T | 3_prime_UTR_variant | 29/29 | ENST00000390654.8 | ||
LOC112267937 | XR_002956237.2 | n.3087G>A | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL23A1 | ENST00000390654.8 | c.*357C>T | 3_prime_UTR_variant | 29/29 | 5 | NM_173465.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.361 AC: 54893AN: 152012Hom.: 11521 Cov.: 33
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GnomAD4 exome AF: 0.416 AC: 34024AN: 81766Hom.: 7758 Cov.: 0 AF XY: 0.425 AC XY: 18551AN XY: 43674
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GnomAD4 genome ? AF: 0.361 AC: 54892AN: 152130Hom.: 11517 Cov.: 33 AF XY: 0.363 AC XY: 26966AN XY: 74366
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at