Variant chr17-48530455-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_002144.4(HOXB1):c.450G>A(p.Ala150=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 1,613,872 control chromosomes in the GnomAD database, including 32,419 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2557 hom., cov: 32)

Exomes 𝑓: 0.20 ( 29862 hom. )

Consequence

HOXB1
NM_002144.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.128

Variant links:

Genes affected

HOXB1 (HGNC:5111): (homeobox B1) This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXB genes located in a cluster on chromosome 17. [provided by RefSeq, Jul 2008]

HOXB1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 17-48530455-C-T is Benign according to our data. Variant chr17-48530455-C-T is described in ClinVar as [Benign]. Clinvar id is 1281602.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-48530455-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.128 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HOXB1	NM_002144.4 linkuse as main transcript	c.450G>A	p.Ala150=	synonymous_variant	1/2	ENST00000239174.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HOXB1	ENST00000239174.7 linkuse as main transcript	c.450G>A	p.Ala150=	synonymous_variant	1/2	1	NM_002144.4	P1	P14653-1
HOXB1	ENST00000577092.1 linkuse as main transcript	c.450G>A	p.Ala150=	synonymous_variant	1/1				P14653-2

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26779

AN:

151960

Hom.:

2557

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.319

Gnomad AMR

AF:

0.155

Gnomad ASJ

AF:

0.190

Gnomad EAS

AF:

0.0871

Gnomad SAS

AF:

0.136

Gnomad FIN

AF:

0.226

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.213

Gnomad OTH

AF:

0.194

GnomAD3 exomes

AF:

0.175

AC:

44006

AN:

251286

Hom.:

4226

AF XY:

0.177

AC XY:

23980

AN XY:

135806

show subpopulations

Gnomad AFR exome

AF:

0.118

Gnomad AMR exome

AF:

0.123

Gnomad ASJ exome

AF:

0.201

Gnomad EAS exome

AF:

0.0889

Gnomad SAS exome

AF:

0.128

Gnomad FIN exome

AF:

0.224

Gnomad NFE exome

AF:

0.213

Gnomad OTH exome

AF:

0.192

GnomAD4 exome

AF:

0.198

AC:

289492

AN:

1461794

Hom.:

29862

Cov.:

AF XY:

0.196

AC XY:

142803

AN XY:

727196

show subpopulations

Gnomad4 AFR exome

AF:

0.120

Gnomad4 AMR exome

AF:

0.127

Gnomad4 ASJ exome

AF:

0.204

Gnomad4 EAS exome

AF:

0.0575

Gnomad4 SAS exome

AF:

0.130

Gnomad4 FIN exome

AF:

0.223

Gnomad4 NFE exome

AF:

0.213

Gnomad4 OTH exome

AF:

0.191

GnomAD4 genome

AF:

0.176

AC:

26788

AN:

152078

Hom.:

2557

Cov.:

AF XY:

0.175

AC XY:

13029

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.122

Gnomad4 AMR

AF:

0.155

Gnomad4 ASJ

AF:

0.190

Gnomad4 EAS

AF:

0.0867

Gnomad4 SAS

AF:

0.137

Gnomad4 FIN

AF:

0.226

Gnomad4 NFE

AF:

0.213

Gnomad4 OTH

AF:

0.191

Alfa

AF:

0.202

Hom.:

4524

Bravo

AF:

0.168

Asia WGS

AF:

0.138

AC:

479

AN:

3478

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	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

1.9

DANN

Benign

0.57

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