Variant chr12-57695630-A-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_006812.4(OS9):c.340-150A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 722,874 control chromosomes in the GnomAD database, including 132,211 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 0.57 ( 26037 hom., cov: 31)

Exomes 𝑓: 0.60 ( 106174 hom. )

Consequence

OS9
NM_006812.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.125

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 = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OS9	NM_006812.4 linkuse as main transcript	c.340-150A>T		intron_variant		ENST00000315970.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OS9	ENST00000315970.12 linkuse as main transcript	c.340-150A>T		intron_variant		1	NM_006812.4	P4	Q13438-1
	ENST00000549477.1 linkuse as main transcript	n.535-1334T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.575

AC:

87212

AN:

151804

Hom.:

26042

Cov.:

show subpopulations

Gnomad AFR

AF:

0.429

Gnomad AMI

AF:

0.493

Gnomad AMR

AF:

0.634

Gnomad ASJ

AF:

0.678

Gnomad EAS

AF:

0.349

Gnomad SAS

AF:

0.390

Gnomad FIN

AF:

0.595

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.670

Gnomad OTH

AF:

0.628

GnomAD4 exome

AF:

0.597

AC:

340795

AN:

570950

Hom.:

106174

Cov.:

AF XY:

0.587

AC XY:

181581

AN XY:

309156

show subpopulations

Gnomad4 AFR exome

AF:

0.421

Gnomad4 AMR exome

AF:

0.619

Gnomad4 ASJ exome

AF:

0.675

Gnomad4 EAS exome

AF:

0.285

Gnomad4 SAS exome

AF:

0.394

Gnomad4 FIN exome

AF:

0.612

Gnomad4 NFE exome

AF:

0.666

Gnomad4 OTH exome

AF:

0.611

GnomAD4 genome

AF:

0.574

AC:

87234

AN:

151924

Hom.:

26037

Cov.:

AF XY:

0.567

AC XY:

42108

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.429

Gnomad4 AMR

AF:

0.634

Gnomad4 ASJ

AF:

0.678

Gnomad4 EAS

AF:

0.350

Gnomad4 SAS

AF:

0.387

Gnomad4 FIN

AF:

0.595

Gnomad4 NFE

AF:

0.670

Gnomad4 OTH

AF:

0.625

Alfa

AF:

0.488

Hom.:

1418

Bravo

AF:

0.573

Asia WGS

AF:

0.388

AC:

1352

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

DANN

Benign

0.80

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.28

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.28

Position offset: -2

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