GeneBe

rs2057482

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000557538.5(HIF1A):​n.2827T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

HIF1A
ENST00000557538.5 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.54

Publications

86 publications found
Variant links:
Genes affected
HIF1A (HGNC:4910): (hypoxia inducible factor 1 subunit alpha) This gene encodes the alpha subunit of transcription factor hypoxia-inducible factor-1 (HIF-1), which is a heterodimer composed of an alpha and a beta subunit. HIF-1 functions as a master regulator of cellular and systemic homeostatic response to hypoxia by activating transcription of many genes, including those involved in energy metabolism, angiogenesis, apoptosis, and other genes whose protein products increase oxygen delivery or facilitate metabolic adaptation to hypoxia. HIF-1 thus plays an essential role in embryonic vascularization, tumor angiogenesis and pathophysiology of ischemic disease. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jul 2011]
HIF1A-AS2 (HGNC:43015): (HIF1A antisense RNA 2)
HIF1A-AS3 (HGNC:54284): (HIF1A antisense RNA 3)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557538.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
HIF1A
NM_001530.4
MANE Select
c.*45T>A
3_prime_UTR
Exon 15 of 15NP_001521.1
HIF1A-AS2
NR_045406.1
n.1960A>T
non_coding_transcript_exon
Exon 1 of 1
HIF1A
NM_001243084.2
c.*45T>A
3_prime_UTR
Exon 15 of 15NP_001230013.1

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
HIF1A
ENST00000557538.5
TSL:1
n.2827T>A
non_coding_transcript_exon
Exon 15 of 15
HIF1A
ENST00000337138.9
TSL:1 MANE Select
c.*45T>A
3_prime_UTR
Exon 15 of 15ENSP00000338018.4
HIF1A
ENST00000539097.2
TSL:1
c.*45T>A
3_prime_UTR
Exon 15 of 15ENSP00000437955.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
1397756
Hom.:
0
Cov.:
22
AF XY:
0.00
AC XY:
0
AN XY:
695450
African (AFR)
AF:
0.00
AC:
0
AN:
31032
American (AMR)
AF:
0.00
AC:
0
AN:
35510
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
22960
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39288
South Asian (SAS)
AF:
0.00
AC:
0
AN:
77950
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
51888
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5488
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1075870
Other (OTH)
AF:
0.00
AC:
0
AN:
57770
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.39
CADD
Benign
16
DANN
Benign
0.91
PhyloP100
3.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
0.97

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2057482; hg19: chr14-62213848; API