11-75566217-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001235.5(SERPINH1):c.-34-99C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000822 in 1,107,036 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0036 ( 5 hom., cov: 33)
Exomes 𝑓: 0.00037 ( 4 hom. )
Consequence
SERPINH1
NM_001235.5 intron
NM_001235.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.641
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 Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 11-75566217-C-T is Benign according to our data. Variant chr11-75566217-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1203092.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINH1 | NM_001235.5 | c.-34-99C>T | intron_variant | ENST00000358171.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINH1 | ENST00000358171.8 | c.-34-99C>T | intron_variant | 1 | NM_001235.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00364 AC: 554AN: 152192Hom.: 6 Cov.: 33
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GnomAD4 exome AF: 0.000375 AC: 358AN: 954726Hom.: 4 AF XY: 0.000331 AC XY: 161AN XY: 485796
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GnomAD4 genome ? AF: 0.00362 AC: 552AN: 152310Hom.: 5 Cov.: 33 AF XY: 0.00311 AC XY: 232AN XY: 74480
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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 | GeneDx | Jan 13, 2019 | - - |
Computational scores
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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