rs10146037

Variant names:

• chr14-61693802-T-C
• rs10146037
• ENST00000557544.3:n.545+1905A>G

Variant summary

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

The ENST00000557544.3(ENSG00000258667):​n.545+1905A>G variant causes a intron 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: ENSG00000258667 ENST00000557544.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549
• Publications: 2 publications found

Genes affected

ENSG00000258667 (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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557544.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIF1A-AS1	NR_047116.1		n.117+1905A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258667	ENST00000557544.3	TSL:3	n.545+1905A>G		intron	N/A
	ENSG00000258667	ENST00000715697.1		n.264+4731A>G		intron	N/A
	ENSG00000258667	ENST00000733788.1		n.215-12227A>G		intron	N/A

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

African (AFR) AF: 0.404 AC: 16756 AN: 41468

American (AMR) AF: 0.0901 AC: 1379 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0772 AC: 268 AN: 3470

East Asian (EAS) AF: 0.00597 AC: 31 AN: 5190

South Asian (SAS) AF: 0.0528 AC: 255 AN: 4828

European-Finnish (FIN) AF: 0.0205 AC: 218 AN: 10616

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0463 AC: 3149 AN: 68026

Other (OTH) AF: 0.141 AC: 298 AN: 2116

Alfa AF: 0.0918 Hom.: 687

Bravo AF: 0.163

Asia WGS AF: 0.0480 AC: 166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.63
PhyloP100		0.55
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10146037; hg19: chr14-62160520;