Variant 12-57698305-C-CACTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000315970.12(OS9):c.579+1933_579+1936dup variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.60 ( 28266 hom., cov: 0)

Consequence

OS9
ENST00000315970.12 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.278

Variant links:

Genes affected

OS9 (HGNC:16994): (OS9 endoplasmic reticulum lectin) This gene encodes a protein that is highly expressed in osteosarcomas. This protein binds to the hypoxia-inducible factor 1 (HIF-1), a key regulator of the hypoxic response and angiogenesis, and promotes the degradation of one of its subunits. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

OS9 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OS9	NM_006812.4 linkuse as main transcript	c.579+1933_579+1936dup		intron_variant		ENST00000315970.12	NP_006803.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OS9	ENST00000315970.12 linkuse as main transcript	c.579+1933_579+1936dup		intron_variant		1	NM_006812.4	ENSP00000318165	P4	Q13438-1
	ENST00000549477.1 linkuse as main transcript	n.535-4010_535-4009insAAGT		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.604

AC:

91558

AN:

151488

Hom.:

28257

Cov.:

show subpopulations

Gnomad AFR

AF:

0.515

Gnomad AMI

AF:

0.531

Gnomad AMR

AF:

0.643

Gnomad ASJ

AF:

0.699

Gnomad EAS

AF:

0.351

Gnomad SAS

AF:

0.455

Gnomad FIN

AF:

0.619

Gnomad MID

AF:

0.709

Gnomad NFE

AF:

0.672

Gnomad OTH

AF:

0.640

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

GnomAD4 genome

AF:

0.604

AC:

91607

AN:

151606

Hom.:

28266

Cov.:

AF XY:

0.598

AC XY:

44282

AN XY:

74066

show subpopulations

Gnomad4 AFR

AF:

0.515

Gnomad4 AMR

AF:

0.643

Gnomad4 ASJ

AF:

0.699

Gnomad4 EAS

AF:

0.351

Gnomad4 SAS

AF:

0.453

Gnomad4 FIN

AF:

0.619

Gnomad4 NFE

AF:

0.672

Gnomad4 OTH

AF:

0.640

Alfa

AF:

0.629

Hom.:

3706

Bravo

AF:

0.602

Asia WGS

AF:

0.441

AC:

1535

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over