ENST00000733794.1:n.306+964C>G

Variant names:

• chr14-61680493-G-C
• rs798847
• ENST00000733794.1:n.306+964C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000733794.1(HIF1A-AS3):​n.306+964C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,166 control chromosomes in the GnomAD database, including 48,929 homozygotes. 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: 𝑓 0.75 (48929 hom., cov: 32)
• Consequence: HIF1A-AS3 ENST00000733794.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387
• Publications: 3 publications found

Genes affected

HIF1A-AS3 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HIF1A-AS3	ENST00000733794.1	n.306+964C>G		intron_variant	Intron 2 of 2
HIF1A-AS3	ENST00000733795.1	n.332+964C>G		intron_variant	Intron 3 of 3
HIF1A-AS3	ENST00000733796.1	n.532+673C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113904 AN: 152048 Hom.: 48917 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.782

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.749 AC: 113957 AN: 152166 Hom.: 48929 Cov.: 32 AF XY: 0.754 AC XY: 56094 AN XY: 74408

African (AFR) AF: 0.292 AC: 12086 AN: 41446

American (AMR) AF: 0.867 AC: 13254 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2987 AN: 3472

East Asian (EAS) AF: 0.831 AC: 4316 AN: 5192

South Asian (SAS) AF: 0.825 AC: 3978 AN: 4820

European-Finnish (FIN) AF: 0.973 AC: 10326 AN: 10618

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 64288 AN: 68024

Other (OTH) AF: 0.783 AC: 1651 AN: 2108

Alfa AF: 0.775 Hom.: 3028

Bravo AF: 0.723

Asia WGS AF: 0.813 AC: 2825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.2
DANN	Benign	0.50
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs798847; hg19: chr14-62147211;