rs137989705
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_153704.6(TMEM67):āc.2010A>Gā(p.Thr670=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000182 in 1,614,138 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. T670T) has been classified as Likely benign.
Frequency
Consequence
NM_153704.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM67 | NM_153704.6 | c.2010A>G | p.Thr670= | synonymous_variant | 20/28 | ENST00000453321.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM67 | ENST00000453321.8 | c.2010A>G | p.Thr670= | synonymous_variant | 20/28 | 1 | NM_153704.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00115 AC: 175AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000259 AC: 65AN: 251394Hom.: 0 AF XY: 0.000132 AC XY: 18AN XY: 135870
GnomAD4 exome AF: 0.0000807 AC: 118AN: 1461774Hom.: 2 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 727190
GnomAD4 genome AF: 0.00115 AC: 175AN: 152364Hom.: 0 Cov.: 33 AF XY: 0.00119 AC XY: 89AN XY: 74506
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 07, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at