14-61740839-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_001530.4(HIF1A):c.1744C>T(p.Pro582Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0954 in 1,613,808 control chromosomes in the GnomAD database, including 7,963 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001530.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIF1A | NM_001530.4 | c.1744C>T | p.Pro582Ser | missense_variant | 12/15 | ENST00000337138.9 | |
HIF1A-AS3 | NR_144368.1 | n.213+10046G>A | intron_variant, non_coding_transcript_variant | ||||
HIF1A | NM_001243084.2 | c.1816C>T | p.Pro606Ser | missense_variant | 12/15 | ||
HIF1A | NM_181054.3 | c.1744C>T | p.Pro582Ser | missense_variant | 12/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIF1A | ENST00000337138.9 | c.1744C>T | p.Pro582Ser | missense_variant | 12/15 | 1 | NM_001530.4 | P4 | |
HIF1A-AS3 | ENST00000660325.2 | n.215+10046G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0782 AC: 11893AN: 152074Hom.: 548 Cov.: 32
GnomAD3 exomes AF: 0.0881 AC: 22150AN: 251470Hom.: 1162 AF XY: 0.0928 AC XY: 12614AN XY: 135912
GnomAD4 exome AF: 0.0973 AC: 142148AN: 1461616Hom.: 7416 Cov.: 32 AF XY: 0.0983 AC XY: 71461AN XY: 727128
GnomAD4 genome ? AF: 0.0781 AC: 11883AN: 152192Hom.: 547 Cov.: 32 AF XY: 0.0757 AC XY: 5630AN XY: 74404
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 22, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | May 25, 2023 | BS1, BP4 - |
Cholangiocarcinoma Other:1
other, no assertion criteria provided | research | Department of Surgery, Campus Charité Mitte Campus Virchow-klinikum, Charite-Universitaetsmedizin Berlin | Dec 10, 2022 | No association with disease-free or overall survival after resection of intrahepatic Cholangiocarcinoma No association with disease-free or overall survival |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at