11-85631688-T-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_018480.7(TMEM126B):āc.83T>Cā(p.Val28Ala) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000469 in 1,607,026 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. V28V) has been classified as Likely benign.
Frequency
Consequence
NM_018480.7 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM126B | NM_018480.7 | c.83T>C | p.Val28Ala | missense_variant, splice_region_variant | 2/5 | ENST00000358867.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM126B | ENST00000358867.11 | c.83T>C | p.Val28Ala | missense_variant, splice_region_variant | 2/5 | 2 | NM_018480.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00269 AC: 409AN: 152078Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000639 AC: 156AN: 244132Hom.: 2 AF XY: 0.000523 AC XY: 69AN XY: 132020
GnomAD4 exome AF: 0.000236 AC: 344AN: 1454830Hom.: 1 Cov.: 31 AF XY: 0.000185 AC XY: 134AN XY: 723536
GnomAD4 genome AF: 0.00269 AC: 410AN: 152196Hom.: 1 Cov.: 33 AF XY: 0.00262 AC XY: 195AN XY: 74406
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 10, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 11, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | TMEM126B: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at