chr3-57198305-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_003865.3(HESX1):c.460-10T>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000413 in 1,451,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003865.3 splice_polypyrimidine_tract, intron
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HESX1 | NM_003865.3 | c.460-10T>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000295934.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HESX1 | ENST00000295934.8 | c.460-10T>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003865.3 | P1 | |||
HESX1 | ENST00000473921.2 | c.358-10T>A | splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
HESX1 | ENST00000647958.1 | c.460-10T>A | splice_polypyrimidine_tract_variant, intron_variant | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000413 AC: 6AN: 1451082Hom.: 0 Cov.: 28 AF XY: 0.00000415 AC XY: 3AN XY: 722606
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Septo-optic dysplasia sequence;C2750027:Growth hormone deficiency with pituitary anomalies Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.