Variant 22-50201141-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_031454.2(SELENOO):c.105C>G(p.Gly35Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00704 in 1,301,496 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0059 ( 2 hom., cov: 34)

Exomes 𝑓: 0.0072 ( 30 hom. )

Consequence

SELENOO
NM_031454.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.910

Variant links:

Genes affected

SELENOO (HGNC:30395): (selenoprotein O) This gene encodes a selenoprotein that is localized to the mitochondria. It is the largest mammalian selenoprotein, containing the rare amino acid selenocysteine (Sec). Sec is encoded by the UGA codon, which normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. The exact function of this selenoprotein is not known, but it is thought to have redox activity. [provided by RefSeq, Dec 2016]

SELENOO links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP6

Variant 22-50201141-C-G is Benign according to our data. Variant chr22-50201141-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2653367.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.91 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00719 (8263/1149852) while in subpopulation MID AF= 0.0224 (73/3262). AF 95% confidence interval is 0.0183. There are 30 homozygotes in gnomad4_exome. There are 4048 alleles in male gnomad4_exome subpopulation. Median coverage is 35. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SELENOO	NM_031454.2 linkuse as main transcript	c.105C>G	p.Gly35Gly	synonymous_variant	1/9	ENST00000380903.7	NP_113642.1	Q9BVL4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SELENOO	ENST00000380903.7 linkuse as main transcript	c.105C>G	p.Gly35Gly	synonymous_variant	1/9	1	NM_031454.2	ENSP00000370288.2		Q9BVL4

Frequencies

GnomAD3 genomes

AF:

0.00589

AC:

893

AN:

151536

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00131

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00742

Gnomad ASJ

AF:

0.0213

Gnomad EAS

AF:

0.000965

Gnomad SAS

AF:

0.00683

Gnomad FIN

AF:

0.00764

Gnomad MID

AF:

0.0192

Gnomad NFE

AF:

0.00759

Gnomad OTH

AF:

0.00675

GnomAD3 exomes

AF:

0.00755

AC:

116

AN:

15360

Hom.:

AF XY:

0.00822

AC XY:

AN XY:

9738

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00456

Gnomad ASJ exome

AF:

0.0224

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00618

Gnomad FIN exome

AF:

0.00962

Gnomad NFE exome

AF:

0.00543

Gnomad OTH exome

AF:

0.00493

GnomAD4 exome

AF:

0.00719

AC:

8263

AN:

1149852

Hom.:

Cov.:

AF XY:

0.00726

AC XY:

4048

AN XY:

557582

show subpopulations

Gnomad4 AFR exome

AF:

0.00110

Gnomad4 AMR exome

AF:

0.00475

Gnomad4 ASJ exome

AF:

0.0202

Gnomad4 EAS exome

AF:

0.0000380

Gnomad4 SAS exome

AF:

0.00652

Gnomad4 FIN exome

AF:

0.00665

Gnomad4 NFE exome

AF:

0.00731

Gnomad4 OTH exome

AF:

0.00733

GnomAD4 genome

AF:

0.00590

AC:

894

AN:

151644

Hom.:

Cov.:

AF XY:

0.00593

AC XY:

440

AN XY:

74140

show subpopulations

Gnomad4 AFR

AF:

0.00130

Gnomad4 AMR

AF:

0.00741

Gnomad4 ASJ

AF:

0.0213

Gnomad4 EAS

AF:

0.000967

Gnomad4 SAS

AF:

0.00725

Gnomad4 FIN

AF:

0.00764

Gnomad4 NFE

AF:

0.00758

Gnomad4 OTH

AF:

0.00668

Alfa

AF:

0.00598

Hom.:

Bravo

AF:

0.00547

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

SELENOO: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

6.4

DANN

Benign

0.86

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over