chr12-54962877-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001136030.3(TESPA1):āc.1021C>Gā(p.Gln341Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,434 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001136030.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TESPA1 | NM_001136030.3 | c.1021C>G | p.Gln341Glu | missense_variant | 9/11 | ENST00000449076.6 | NP_001129502.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TESPA1 | ENST00000449076.6 | c.1021C>G | p.Gln341Glu | missense_variant | 9/11 | 2 | NM_001136030.3 | ENSP00000400892 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248824Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134980
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461434Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726942
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.1021C>G (p.Q341E) alteration is located in exon 9 (coding exon 8) of the TESPA1 gene. This alteration results from a C to G substitution at nucleotide position 1021, causing the glutamine (Q) at amino acid position 341 to be replaced by a glutamic acid (E). 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