rs397517868
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_147196.3(TMIE):c.388_391delinsG(p.Lys130_Lys131delinsGlu) variant causes a protein altering change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. K130K) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Consequence
TMIE
NM_147196.3 protein_altering
NM_147196.3 protein_altering
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.51
Genes affected
TMIE (HGNC:30800): (transmembrane inner ear) This gene encodes a transmembrane inner ear protein. Studies in mouse suggest that this gene is required for normal postnatal maturation of sensory hair cells in the cochlea, including correct development of stereocilia bundles. This gene is one of multiple genes responsible for recessive non-syndromic deafness (DFNB), also known as autosomal recessive nonsyndromic hearing loss (ARNSHL), the most common form of congenitally acquired inherited hearing impairment. [provided by RefSeq, Mar 2009]
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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;
BP6
?
Variant 3-46709605-AAGA-G is Benign according to our data. Variant chr3-46709605-AAGA-G is described in ClinVar as [Likely_benign]. Clinvar id is 47961.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMIE | NM_147196.3 | c.388_391delinsG | p.Lys130_Lys131delinsGlu | protein_altering_variant | 4/4 | ENST00000643606.3 | |
TMIE | NM_001370524.1 | c.229_232delinsG | p.Lys77_Lys78delinsGlu | protein_altering_variant | 4/4 | ||
TMIE | NM_001370525.1 | c.229_232delinsG | p.Lys77_Lys78delinsGlu | protein_altering_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMIE | ENST00000643606.3 | c.388_391delinsG | p.Lys130_Lys131delinsGlu | protein_altering_variant | 4/4 | NM_147196.3 | P1 | ||
TMIE | ENST00000644830.1 | c.229_232delinsG | p.Lys77_Lys78delinsGlu | protein_altering_variant | 4/4 | ||||
TMIE | ENST00000651652.1 | c.*310_*313delinsG | 3_prime_UTR_variant | 2/2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 30, 2012 | Lys130_Lys131delinsGlu in exon 4 of TMIE: This variant represents a missense cha nge, Lys131Glu (dbSNP ID rs201683042), that arose on the background of the very common benign variant Lys131del (dbSNP ID rs10578999). Neither variant, nor the combination of variants, is expected to impact the protein as the 3 bp deletion is extremely common and the missense change occurs in a mammal (rabbit has the L ys131Glu in its normal TMIE protein). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at