rs779093042
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004568.6(SERPINB6):c.-3A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,461,680 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 Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000020 ( 0 hom. )
Consequence
SERPINB6
NM_004568.6 5_prime_UTR
NM_004568.6 5_prime_UTR
Scores
10
Clinical Significance
Conservation
PhyloP100: -0.603
Genes affected
SERPINB6 (HGNC:8950): (serpin family B member 6) The protein encoded by this gene is a member of the serpin (serine proteinase inhibitor) superfamily, and ovalbumin(ov)-serpin subfamily. It was originally discovered as a placental thrombin inhibitor. The mouse homolog was found to be expressed in the hair cells of the inner ear. Mutations in this gene are associated with nonsyndromic progressive hearing loss, suggesting that this serpin plays an important role in the inner ear in the protection against leakage of lysosomal content during stress, and that loss of this protection results in cell death and sensorineural hearing loss. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.13044444).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINB6 | NM_004568.6 | c.-3A>G | 5_prime_UTR_variant | 2/7 | ENST00000380539.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINB6 | ENST00000380539.7 | c.-3A>G | 5_prime_UTR_variant | 2/7 | 3 | NM_004568.6 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251282Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135842
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GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461680Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 727170
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GnomAD4 genome Cov.: 32
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32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Oct 04, 2015 | Variant classified as Uncertain Significance - Favor Benign. The c.-3A>G variant in SERPINB6 has not been previously reported in individuals with hearing loss, but has been identified in 1/66614 of European chromosomes by the Exome Aggregat ion Consortium (ExAC, http://exac.broadinstitute.org). The variant is located in the initiator sequence of the 5?untranslated region (5'UTR) and variants in thi s region could have an effect on transcriptional or translational regulation. Ho wever, this nucleotide position is not conserved across species with several mam mals and distant species having a guanine (G) at this position, suggesting that this variant may be tolerated. Please note that this variant leads to a missense variant (p.Ile4Val, p.Ile14Val, or p.Ile19Val) in three different transcript is oforms of the SERPINB6. Computational and conservation data suggest this missens e change in the transcript isoforms would not impact the protein, however this i nformation is not sufficient to rule out pathogenicity. In summary, while the cl inical significance of the c.-3A>G variant is uncertain, these data suggest that it is more likely to be benign. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;T
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;.;T
MetaRNN
Benign
T;T;T
MutationTaster
Benign
N;N;N;N;N;N
PrimateAI
Benign
T
Sift4G
Benign
T;.;.
Vest4
MVP
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
gMVP
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