Variant rs2301720 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_006896.4(HOXA7):c.96T>G(p.Ala32=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 1,613,554 control chromosomes in the GnomAD database, including 588,711 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.79 ( 48027 hom., cov: 37)

Exomes 𝑓: 0.86 ( 540684 hom. )

Consequence

HOXA7
NM_006896.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.603

Variant links:

Genes affected

HOXA7 (HGNC:5108): (homeobox A7) In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. For example, the encoded protein represses the transcription of differentiation-specific genes during keratinocyte proliferation, but this repression is then overcome by differentiation signals. This gene is highly similar to the antennapedia (Antp) gene of Drosophila. [provided by RefSeq, Jul 2008]

HOXA7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BP7

Synonymous conserved (PhyloP=0.603 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HOXA7	NM_006896.4 linkuse as main transcript	c.96T>G	p.Ala32=	synonymous_variant	1/2	ENST00000242159.5	NP_008827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HOXA7	ENST00000242159.5 linkuse as main transcript	c.96T>G	p.Ala32=	synonymous_variant	1/2	1	NM_006896.4	ENSP00000242159	P1
HOXA7	ENST00000519842.1 linkuse as main transcript			downstream_gene_variant		3		ENSP00000428563

Frequencies

GnomAD3 genomes

AF:

0.786

AC:

119625

AN:

152150

Hom.:

48005

Cov.:

show subpopulations

Gnomad AFR

AF:

0.612

Gnomad AMI

AF:

0.929

Gnomad AMR

AF:

0.766

Gnomad ASJ

AF:

0.918

Gnomad EAS

AF:

0.852

Gnomad SAS

AF:

0.879

Gnomad FIN

AF:

0.816

Gnomad MID

AF:

0.892

Gnomad NFE

AF:

0.870

Gnomad OTH

AF:

0.816

GnomAD3 exomes

AF:

0.832

AC:

207706

AN:

249718

Hom.:

87208

AF XY:

0.841

AC XY:

114113

AN XY:

135614

show subpopulations

Gnomad AFR exome

AF:

0.595

Gnomad AMR exome

AF:

0.728

Gnomad ASJ exome

AF:

0.924

Gnomad EAS exome

AF:

0.866

Gnomad SAS exome

AF:

0.880

Gnomad FIN exome

AF:

0.820

Gnomad NFE exome

AF:

0.870

Gnomad OTH exome

AF:

0.849

GnomAD4 exome

AF:

0.859

AC:

1254641

AN:

1461288

Hom.:

540684

Cov.:

AF XY:

0.860

AC XY:

625328

AN XY:

726856

show subpopulations

Gnomad4 AFR exome

AF:

0.605

Gnomad4 AMR exome

AF:

0.728

Gnomad4 ASJ exome

AF:

0.921

Gnomad4 EAS exome

AF:

0.855

Gnomad4 SAS exome

AF:

0.877

Gnomad4 FIN exome

AF:

0.827

Gnomad4 NFE exome

AF:

0.870

Gnomad4 OTH exome

AF:

0.853

GnomAD4 genome

AF:

0.786

AC:

119696

AN:

152266

Hom.:

48027

Cov.:

AF XY:

0.785

AC XY:

58457

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.612

Gnomad4 AMR

AF:

0.765

Gnomad4 ASJ

AF:

0.918

Gnomad4 EAS

AF:

0.852

Gnomad4 SAS

AF:

0.880

Gnomad4 FIN

AF:

0.816

Gnomad4 NFE

AF:

0.871

Gnomad4 OTH

AF:

0.817

Alfa

AF:

0.851

Hom.:

71292

Bravo

AF:

0.770

Asia WGS

AF:

0.865

AC:

3008

AN:

3478

EpiCase

AF:

0.877

EpiControl

AF:

0.870

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

DANN

Benign

0.77

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over