chr14-20454990-T-G

Position:

• chr14-20454990-T-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000556439.1(OSGEP):​n.100A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 478,654 control chromosomes in the GnomAD database, including 90,467 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.63 (30163 hom., cov: 33)
  • Exomes 𝑓: 0.60 (60304 hom.)
• Consequence: OSGEP ENST00000556439.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.119

Genes affected

OSGEP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 14-20454990-T-G is Benign according to our data. Variant chr14-20454990-T-G is described in ClinVar as [Benign]. Clinvar id is 1282032.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.20454990T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OSGEP	ENST00000556252.1	n.64A>C		non_coding_transcript_exon_variant	1/3	3
OSGEP	ENST00000556439.1	n.100A>C		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95098 AN: 151980 Hom.: 30119 Cov.: 33

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.637

GnomAD4 exome AF: 0.604 AC: 197113 AN: 326556 Hom.: 60304 Cov.: 0 AF XY: 0.602 AC XY: 102839 AN XY: 170924

Gnomad4 AFR exome AF: 0.704

Gnomad4 AMR exome AF: 0.488

Gnomad4 ASJ exome AF: 0.655

Gnomad4 EAS exome AF: 0.502

Gnomad4 SAS exome AF: 0.582

Gnomad4 FIN exome AF: 0.689

Gnomad4 NFE exome AF: 0.606

Gnomad4 OTH exome AF: 0.618

GnomAD4 genome AF: 0.626 AC: 95207 AN: 152098 Hom.: 30163 Cov.: 33 AF XY: 0.628 AC XY: 46654 AN XY: 74318

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.637

Alfa AF: 0.599 Hom.: 25363

Bravo AF: 0.615

Asia WGS AF: 0.547 AC: 1904 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 13, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1760944; hg19: chr14-20923149;