Variant X-120115635-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_139282.3(RHOXF1):c.228G>A(p.Glu76Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00308 in 1,179,610 control chromosomes in the GnomAD database, including 77 homozygotes. There are 979 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.016 ( 32 hom., 508 hem., cov: 21)

Exomes 𝑓: 0.0017 ( 45 hom. 471 hem. )

Consequence

RHOXF1
NM_139282.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.348

Variant links:

Genes affected

RHOXF1 (HGNC:29993): (Rhox homeobox family member 1) This gene is a member of the PEPP subfamily of paired-like homoebox genes. The gene may be regulated by androgens and epigenetic mechanisms. The encoded nuclear protein is likely a transcription factor that may play a role in human reproduction. [provided by RefSeq, Dec 2012]

RHOXF1 links:

RHOXF1-AS1 (HGNC:):

RHOXF1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant X-120115635-C-T is Benign according to our data. Variant chrX-120115635-C-T is described in ClinVar as [Benign]. Clinvar id is 777826.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.348 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RHOXF1	NM_139282.3 linkuse as main transcript	c.228G>A	p.Glu76Glu	synonymous_variant	1/3	ENST00000217999.3	NP_644811.1	Q8NHV9
RHOXF1	XM_011531281.3 linkuse as main transcript	c.312G>A	p.Glu104Glu	synonymous_variant	2/4		XP_011529583.1
RHOXF1-AS1	NR_131238.1 linkuse as main transcript	n.298-5217C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
RHOXF1	ENST00000217999.3 linkuse as main transcript	c.228G>A	p.Glu76Glu	synonymous_variant	1/3	1	NM_139282.3	ENSP00000217999.1	Q8NHV9
RHOXF1	ENST00000703667.1 linkuse as main transcript	c.228G>A	p.Glu76Glu	synonymous_variant	7/9			ENSP00000515423.1	Q8NHV9
RHOXF1-AS1	ENST00000553843.5 linkuse as main transcript	n.298-5217C>T		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0159

AC:

1790

AN:

112764

Hom.:

Cov.:

AF XY:

0.0146

AC XY:

509

AN XY:

34918

show subpopulations

Gnomad AFR

AF:

0.0540

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00759

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000131

Gnomad OTH

AF:

0.0165

GnomAD3 exomes

AF:

0.00520

AC:

783

AN:

150495

Hom.:

AF XY:

0.00352

AC XY:

157

AN XY:

44601

show subpopulations

Gnomad AFR exome

AF:

0.0572

Gnomad AMR exome

AF:

0.00333

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000157

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000735

Gnomad OTH exome

AF:

0.00380

GnomAD4 exome

AF:

0.00172

AC:

1837

AN:

1066794

Hom.:

Cov.:

AF XY:

0.00138

AC XY:

471

AN XY:

342450

show subpopulations

Gnomad4 AFR exome

AF:

0.0577

Gnomad4 AMR exome

AF:

0.00386

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000201

Gnomad4 FIN exome

AF:

0.0000265

Gnomad4 NFE exome

AF:

0.0000375

Gnomad4 OTH exome

AF:

0.00423

GnomAD4 genome

AF:

0.0159

AC:

1791

AN:

112816

Hom.:

Cov.:

AF XY:

0.0145

AC XY:

508

AN XY:

34980

show subpopulations

Gnomad4 AFR

AF:

0.0540

Gnomad4 AMR

AF:

0.00758

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000131

Gnomad4 OTH

AF:

0.0163

Alfa

AF:

0.00773

Hom.:

Bravo

AF:

0.0193

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

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	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.5

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