10-101131563-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005521.4(TLX1):c.22C>T(p.His8Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000425 in 1,527,812 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005521.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TLX1 | NM_005521.4 | c.22C>T | p.His8Tyr | missense_variant | Exon 1 of 3 | ENST00000370196.11 | NP_005512.1 | |
TLX1 | NM_001195517.2 | c.22C>T | p.His8Tyr | missense_variant | Exon 1 of 3 | NP_001182446.1 | ||
TLX1 | XM_011539744.4 | c.22C>T | p.His8Tyr | missense_variant | Exon 1 of 3 | XP_011538046.1 | ||
TLX1NB | NR_130724.1 | n.580-4465G>A | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TLX1 | ENST00000370196.11 | c.22C>T | p.His8Tyr | missense_variant | Exon 1 of 3 | 1 | NM_005521.4 | ENSP00000359215.6 | ||
TLX1 | ENST00000467928.2 | c.22C>T | p.His8Tyr | missense_variant | Exon 1 of 3 | 1 | ENSP00000434914.2 | |||
TLX1 | ENST00000463716.3 | c.-165C>T | upstream_gene_variant | 3 | ENSP00000434358.3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152112Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000422 AC: 58AN: 1375700Hom.: 0 Cov.: 31 AF XY: 0.0000395 AC XY: 27AN XY: 682868
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.22C>T (p.H8Y) alteration is located in exon 1 (coding exon 1) of the TLX1 gene. This alteration results from a C to T substitution at nucleotide position 22, causing the histidine (H) at amino acid position 8 to be replaced by a tyrosine (Y). 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