14-61682071-G-C

Variant names:

• chr14-61682071-G-C
• rs2246254
• ENST00000733789.1:n.469C>G

Variant summary

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

The ENST00000733789.1(HIF1A-AS3):​n.469C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,160 control chromosomes in the GnomAD database, including 57,389 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 0.83 (57389 hom., cov: 32)
• Consequence: HIF1A-AS3 ENST00000733789.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 1 publications found

Genes affected

HIF1A-AS3 (HGNC:):

HIF1A-AS1 (HGNC:43014): (HIF1A antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HIF1A-AS1	NR_047116.1	n.118-496C>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HIF1A-AS3	ENST00000733789.1	n.469C>G		non_coding_transcript_exon_variant	Exon 4 of 4
HIF1A-AS3	ENST00000733790.1	n.288C>G		non_coding_transcript_exon_variant	Exon 2 of 2
HIF1A-AS3	ENST00000733798.1	n.277C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126877 AN: 152042 Hom.: 57356 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.987

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.834 AC: 126958 AN: 152160 Hom.: 57389 Cov.: 32 AF XY: 0.841 AC XY: 62566 AN XY: 74412

African (AFR) AF: 0.445 AC: 18438 AN: 41410

American (AMR) AF: 0.922 AC: 14106 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3404 AN: 3472

East Asian (EAS) AF: 0.985 AC: 5113 AN: 5190

South Asian (SAS) AF: 0.988 AC: 4765 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10617 AN: 10618

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.993 AC: 67535 AN: 68030

Other (OTH) AF: 0.860 AC: 1817 AN: 2112

Alfa AF: 0.902 Hom.: 7653

Bravo AF: 0.812

Asia WGS AF: 0.956 AC: 3322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.76
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs2246254; hg19: chr14-62148789;