chr14-61732415-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBS2_Supporting
The NM_001530.4(HIF1A):c.774-3C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0017 in 1,578,296 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001530.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIF1A | NM_001530.4 | c.774-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000337138.9 | |||
HIF1A-AS3 | NR_144368.1 | n.214-15398G>A | intron_variant, non_coding_transcript_variant | ||||
HIF1A | NM_001243084.2 | c.846-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
HIF1A | NM_181054.3 | c.774-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIF1A | ENST00000337138.9 | c.774-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001530.4 | P4 | |||
HIF1A-AS3 | ENST00000660325.2 | n.216-18413G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00123 AC: 187AN: 151954Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00134 AC: 328AN: 244848Hom.: 1 AF XY: 0.00140 AC XY: 185AN XY: 132188
GnomAD4 exome AF: 0.00175 AC: 2491AN: 1426224Hom.: 3 Cov.: 25 AF XY: 0.00171 AC XY: 1217AN XY: 711220
GnomAD4 genome AF: 0.00123 AC: 187AN: 152072Hom.: 0 Cov.: 32 AF XY: 0.00143 AC XY: 106AN XY: 74314
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Mar 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at