3-112042015-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001395507.1(TMPRSS7):c.394G>A(p.Glu132Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000166 in 1,551,460 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001395507.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMPRSS7 | NM_001395507.1 | c.394G>A | p.Glu132Lys | missense_variant | Exon 3 of 18 | ENST00000452346.7 | NP_001382436.1 | |
TMPRSS7 | NM_001042575.2 | c.58G>A | p.Glu20Lys | missense_variant | Exon 2 of 16 | NP_001036040.2 | ||
TMPRSS7 | XM_011512754.2 | c.145G>A | p.Glu49Lys | missense_variant | Exon 2 of 17 | XP_011511056.1 | ||
TMPRSS7 | NR_026734.1 | n.228G>A | non_coding_transcript_exon_variant | Exon 2 of 17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMPRSS7 | ENST00000452346.7 | c.394G>A | p.Glu132Lys | missense_variant | Exon 3 of 18 | 5 | NM_001395507.1 | ENSP00000398236.2 | ||
TMPRSS7 | ENST00000419127.5 | c.58G>A | p.Glu20Lys | missense_variant | Exon 2 of 16 | 1 | ENSP00000411645.1 | |||
TMPRSS7 | ENST00000617607.4 | c.58G>A | p.Glu20Lys | missense_variant | Exon 1 of 15 | 5 | ENSP00000478830.1 | |||
TMPRSS7 | ENST00000435737.5 | n.58G>A | non_coding_transcript_exon_variant | Exon 2 of 17 | 2 | ENSP00000415472.1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000115 AC: 18AN: 156534Hom.: 0 AF XY: 0.0000844 AC XY: 7AN XY: 82954
GnomAD4 exome AF: 0.000173 AC: 242AN: 1399342Hom.: 0 Cov.: 32 AF XY: 0.000177 AC XY: 122AN XY: 690182
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.58G>A (p.E20K) alteration is located in exon 2 (coding exon 1) of the TMPRSS7 gene. This alteration results from a G to A substitution at nucleotide position 58, causing the glutamic acid (E) at amino acid position 20 to be replaced by a lysine (K). 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