7-98851534-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000339375.9(TMEM130):c.893C>T(p.Ala298Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000737 in 1,614,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000339375.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM130 | NM_152913.3 | c.893C>T | p.Ala298Val | missense_variant | 6/8 | ENST00000339375.9 | NP_690877.1 | |
TMEM130 | NM_001134450.2 | c.893C>T | p.Ala298Val | missense_variant | 6/8 | NP_001127922.1 | ||
TMEM130 | NM_001134451.2 | c.587C>T | p.Ala196Val | missense_variant | 5/7 | NP_001127923.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM130 | ENST00000339375.9 | c.893C>T | p.Ala298Val | missense_variant | 6/8 | 1 | NM_152913.3 | ENSP00000341256.4 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152134Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251350Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135852
GnomAD4 exome AF: 0.0000766 AC: 112AN: 1461868Hom.: 0 Cov.: 31 AF XY: 0.0000770 AC XY: 56AN XY: 727232
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152134Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 18, 2021 | The c.893C>T (p.A298V) alteration is located in exon 6 (coding exon 6) of the TMEM130 gene. This alteration results from a C to T substitution at nucleotide position 893, causing the alanine (A) at amino acid position 298 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at