rs10146037

Positions:

• chr14-61693802-T-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.117+1905A>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 0.147 in 152,222 control chromosomes in the GnomAD database, including 3,526 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 0.15 (3526 hom., cov: 33)
• Consequence: HIF1A-AS1 NR_047116.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HIF1A-AS1	NR_047116.1	n.117+1905A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HIF1A-AS1	ENST00000557544.2	n.186+1905A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22367 AN: 152104 Hom.: 3519 Cov.: 33

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0902

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.00596

Gnomad SAS AF: 0.0528

Gnomad FIN AF: 0.0205

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0463

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.147 AC: 22407 AN: 152222 Hom.: 3526 Cov.: 33 AF XY: 0.141 AC XY: 10503 AN XY: 74450

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.0901

Gnomad4 ASJ AF: 0.0772

Gnomad4 EAS AF: 0.00597

Gnomad4 SAS AF: 0.0528

Gnomad4 FIN AF: 0.0205

Gnomad4 NFE AF: 0.0463

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0821 Hom.: 502

Bravo AF: 0.163

Asia WGS AF: 0.0480 AC: 166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10146037; hg19: chr14-62160520;