11-8964219-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020644.3(TMEM9B):c.95A>T(p.Asp32Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000721 in 1,581,498 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D32E) has been classified as Uncertain significance.
Frequency
Consequence
NM_020644.3 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 | UniProt |
---|---|---|---|---|---|---|---|
TMEM9B | NM_020644.3 | c.95A>T | p.Asp32Val | missense_variant | 1/5 | ENST00000534025.6 | |
TMEM9B | NM_001286094.2 | c.-36A>T | 5_prime_UTR_variant | 1/4 | |||
TMEM9B | NM_001286095.2 | c.-118+671A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM9B | ENST00000534025.6 | c.95A>T | p.Asp32Val | missense_variant | 1/5 | 1 | NM_020644.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000411 AC: 8AN: 194576Hom.: 0 AF XY: 0.0000378 AC XY: 4AN XY: 105760
GnomAD4 exome AF: 0.0000742 AC: 106AN: 1429280Hom.: 0 Cov.: 30 AF XY: 0.0000833 AC XY: 59AN XY: 708248
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74420
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 15, 2021 | The c.95A>T (p.D32V) alteration is located in exon 1 (coding exon 1) of the TMEM9B gene. This alteration results from a A to T substitution at nucleotide position 95, causing the aspartic acid (D) at amino acid position 32 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