14-61682071-G-C

Position:

• chr14-61682071-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_047116.1(HIF1A-AS1):​n.118-496C>G variant causes a intron, non coding transcript 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-AS1 NR_047116.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
HIF1A-AS1	NR_047116.1	n.118-496C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HIF1A-AS1	ENST00000557544.2	n.187-496C>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.922

Gnomad4 ASJ AF: 0.980

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.988

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.993

Gnomad4 OTH AF: 0.860

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2246254; hg19: chr14-62148789;