chr11-75566451-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001235.5(SERPINH1):c.102G>A(p.Glu34=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000147 in 1,612,396 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000052 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00016 ( 0 hom. )
Consequence
SERPINH1
NM_001235.5 synonymous
NM_001235.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.192
Genes affected
SERPINH1 (HGNC:1546): (serpin family H member 1) This gene encodes a member of the serpin superfamily of serine proteinase inhibitors. The encoded protein is localized to the endoplasmic reticulum and plays a role in collagen biosynthesis as a collagen-specific molecular chaperone. Autoantibodies to the encoded protein have been found in patients with rheumatoid arthritis. Expression of this gene may be a marker for cancer, and nucleotide polymorphisms in this gene may be associated with preterm birth caused by preterm premature rupture of membranes. Alternatively spliced transcript variants have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, May 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
?
Variant 11-75566451-G-A is Benign according to our data. Variant chr11-75566451-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1594119.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.192 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINH1 | NM_001235.5 | c.102G>A | p.Glu34= | synonymous_variant | 2/5 | ENST00000358171.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINH1 | ENST00000358171.8 | c.102G>A | p.Glu34= | synonymous_variant | 2/5 | 1 | NM_001235.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000525 AC: 8AN: 152282Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000613 AC: 15AN: 244828Hom.: 0 AF XY: 0.0000748 AC XY: 10AN XY: 133662
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GnomAD4 exome AF: 0.000157 AC: 229AN: 1459996Hom.: 0 Cov.: 31 AF XY: 0.000146 AC XY: 106AN XY: 726320
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GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152400Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74534
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 29, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at