chr12-57698305-C-CACTT

Variant names:

• chr12-57698305-C-CACTT
• rs10683701
• NM_006812.4:c.579+1933_579+1936dupACTT

Variant summary

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

The NM_006812.4(OS9):​c.579+1933_579+1936dupACTT 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 NM_006812.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

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]

ENSG00000257342 (HGNC:58278):

ACMG classification

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 rank	MANE	Protein	UniProt
OS9	NM_006812.4	c.579+1933_579+1936dupACTT		intron_variant	Intron 5 of 14	ENST00000315970.12	NP_006803.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OS9	ENST00000315970.12	c.579+1932_579+1933insACTT		intron_variant	Intron 5 of 14	1	NM_006812.4	ENSP00000318165.7

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91558 AN: 151488 Hom.: 28257 Cov.: 0

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.: 0 AF XY: 0.598 AC XY: 44282 AN XY: 74066

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10683701; hg19: chr12-58092088;