chrX-125322683-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001195272.2(TEX13C):c.2564G>A(p.Ser855Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000488 in 512,527 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 83 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 8/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001195272.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEX13C | NM_001195272.2 | c.2564G>A | p.Ser855Asn | missense_variant | 1/2 | ENST00000695840.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEX13C | ENST00000695840.1 | c.2564G>A | p.Ser855Asn | missense_variant | 1/2 | NM_001195272.2 | P1 | ||
TEX13C | ENST00000632600.2 | c.2564G>A | p.Ser855Asn | missense_variant | 1/1 | P1 | |||
TEX13C | ENST00000695841.1 | c.2564G>A | p.Ser855Asn | missense_variant | 1/2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000334 AC: 37AN: 110919Hom.: 0 Cov.: 23 AF XY: 0.000181 AC XY: 6AN XY: 33203
GnomAD3 exomes AF: 0.000409 AC: 40AN: 97904Hom.: 0 AF XY: 0.000382 AC XY: 14AN XY: 36608
GnomAD4 exome AF: 0.000530 AC: 213AN: 401608Hom.: 0 Cov.: 0 AF XY: 0.000517 AC XY: 77AN XY: 149052
GnomAD4 genome ? AF: 0.000334 AC: 37AN: 110919Hom.: 0 Cov.: 23 AF XY: 0.000181 AC XY: 6AN XY: 33203
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | TEX13C: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at