rs35276012
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_152464.3(TMEM199):āc.256T>Cā(p.Tyr86His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00119 in 1,612,660 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_152464.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM199 | NM_152464.3 | c.256T>C | p.Tyr86His | missense_variant | 2/6 | ENST00000292114.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM199 | ENST00000292114.8 | c.256T>C | p.Tyr86His | missense_variant | 2/6 | 1 | NM_152464.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00622 AC: 947AN: 152246Hom.: 9 Cov.: 33
GnomAD3 exomes AF: 0.00168 AC: 420AN: 249436Hom.: 7 AF XY: 0.00119 AC XY: 160AN XY: 134870
GnomAD4 exome AF: 0.000660 AC: 964AN: 1460296Hom.: 14 Cov.: 30 AF XY: 0.000573 AC XY: 416AN XY: 726472
GnomAD4 genome ? AF: 0.00628 AC: 957AN: 152364Hom.: 10 Cov.: 33 AF XY: 0.00601 AC XY: 448AN XY: 74518
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 04, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at