chr3-112063547-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001395507.1(TMPRSS7):c.1470A>T(p.Arg490Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,613,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMPRSS7 | NM_001395507.1 | c.1470A>T | p.Arg490Ser | missense_variant | 12/18 | ENST00000452346.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMPRSS7 | ENST00000452346.7 | c.1470A>T | p.Arg490Ser | missense_variant | 12/18 | 5 | NM_001395507.1 | ||
TMPRSS7 | ENST00000419127.5 | c.1092A>T | p.Arg364Ser | missense_variant | 10/16 | 1 | P1 | ||
TMPRSS7 | ENST00000617607.4 | c.1092A>T | p.Arg364Ser | missense_variant | 9/15 | 5 | P1 | ||
TMPRSS7 | ENST00000435737.5 | c.*815A>T | 3_prime_UTR_variant, NMD_transcript_variant | 11/17 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152066Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000128 AC: 32AN: 249338Hom.: 0 AF XY: 0.0000887 AC XY: 12AN XY: 135258
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461776Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 727196
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152066Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.1092A>T (p.R364S) alteration is located in exon 10 (coding exon 9) of the TMPRSS7 gene. This alteration results from a A to T substitution at nucleotide position 1092, causing the arginine (R) at amino acid position 364 to be replaced by a serine (S). 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