Variant X-120077122-GCCGCCGCCATCTTTTTCTTCT-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM4BP6_ModerateBS2

The ENST00000371402.5(RHOXF2B):c.225_245delAGAAGAAAAAGATGGCGGCGG(p.Glu76_Gly82del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00089 ( 11 hom., 11 hem., cov: 13)

Exomes 𝑓: 0.0013 ( 150 hom. 370 hem. )

Failed GnomAD Quality Control

Consequence

RHOXF2B
ENST00000371402.5 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00

Variant links:

Genes affected

RHOXF2B (HGNC:33519): (Rhox homeobox family member 2B) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in positive regulation of gene expression. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]

RHOXF2B links:

RHOXF1-AS1 (HGNC:):

RHOXF1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in ENST00000371402.5.

BP6

Variant X-120077122-GCCGCCGCCATCTTTTTCTTCT-G is Benign according to our data. Variant chrX-120077122-GCCGCCGCCATCTTTTTCTTCT-G is described in ClinVar as [Likely_benign]. Clinvar id is 2661313.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 11 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RHOXF2B	NM_001099685.3 linkuse as main transcript	c.225_245delAGAAGAAAAAGATGGCGGCGG	p.Glu76_Gly82del	disruptive_inframe_deletion	2/4	ENST00000371402.5	NP_001093155.1	P0C7M4
RHOXF1-AS1	NR_131238.1 linkuse as main transcript	n.297+40617_297+40637delGCCATCTTTTTCTTCTCCGCC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RHOXF2B	ENST00000371402.5 linkuse as main transcript	c.225_245delAGAAGAAAAAGATGGCGGCGG	p.Glu76_Gly82del	disruptive_inframe_deletion	2/4	1	NM_001099685.3	ENSP00000360455.3		P0C7M4
RHOXF1-AS1	ENST00000553843.5 linkuse as main transcript	n.297+40617_297+40637delGCCATCTTTTTCTTCTCCGCC		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.000890

AC:

AN:

85420

Hom.:

Cov.:

AF XY:

0.000549

AC XY:

AN XY:

20040

show subpopulations

Gnomad AFR

AF:

0.000358

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000280

Gnomad ASJ

AF:

0.00240

Gnomad EAS

AF:

0.000457

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00137

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000132

AC:

AN:

151973

Hom.:

AF XY:

0.00

AC XY:

AN XY:

48613

show subpopulations

Gnomad AFR exome

AF:

0.0000907

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000142

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00125

AC:

1210

AN:

964461

Hom.:

150

AF XY:

0.00134

AC XY:

370

AN XY:

275347

show subpopulations

Gnomad4 AFR exome

AF:

0.00135

Gnomad4 AMR exome

AF:

0.000317

Gnomad4 ASJ exome

AF:

0.00180

Gnomad4 EAS exome

AF:

0.0000921

Gnomad4 SAS exome

AF:

0.0000520

Gnomad4 FIN exome

AF:

0.0000784

Gnomad4 NFE exome

AF:

0.00144

Gnomad4 OTH exome

AF:

0.00109

GnomAD4 genome

AF:

0.000890

AC:

AN:

85420

Hom.:

Cov.:

AF XY:

0.000549

AC XY:

AN XY:

20040

show subpopulations

Gnomad4 AFR

AF:

0.000358

Gnomad4 AMR

AF:

0.000280

Gnomad4 ASJ

AF:

0.00240

Gnomad4 EAS

AF:

0.000457

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00137

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00135

Hom.:

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

Apr 01, 2023

RHOXF2B: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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