Variant chr7-27102038-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_006735.4(HOXA2):c.391+72G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 1,580,634 control chromosomes in the GnomAD database, including 99,440 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.27 ( 7329 hom., cov: 31)

Exomes 𝑓: 0.35 ( 92111 hom. )

Consequence

HOXA2
NM_006735.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.520

Variant links:

Genes affected

HOXA2 (HGNC:5103): (homeobox A2) 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. The encoded protein may be involved in the placement of hindbrain segments in the proper location along the anterior-posterior axis during development. [provided by RefSeq, Jul 2008]

HOXA2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 7-27102038-C-G is Benign according to our data. Variant chr7-27102038-C-G is described in ClinVar as [Benign]. Clinvar id is 1289147.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HOXA2	NM_006735.4 link	c.391+72G>C		intron_variant		ENST00000222718.7	NP_006726.1	O43364

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HOXA2	ENST00000222718.7 link	c.391+72G>C		intron_variant		1	NM_006735.4	ENSP00000222718.5		O43364
HOXA2	ENST00000612779.1 link	n.649G>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes

AF:

0.275

AC:

41740

AN:

151958

Hom.:

7330

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0683

Gnomad AMI

AF:

0.359

Gnomad AMR

AF:

0.348

Gnomad ASJ

AF:

0.430

Gnomad EAS

AF:

0.100

Gnomad SAS

AF:

0.264

Gnomad FIN

AF:

0.376

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.298

GnomAD3 exomes

AF:

0.320

AC:

64969

AN:

202938

Hom.:

11805

AF XY:

0.319

AC XY:

35704

AN XY:

111828

show subpopulations

Gnomad AFR exome

AF:

0.0523

Gnomad AMR exome

AF:

0.397

Gnomad ASJ exome

AF:

0.434

Gnomad EAS exome

AF:

0.0968

Gnomad SAS exome

AF:

0.258

Gnomad FIN exome

AF:

0.371

Gnomad NFE exome

AF:

0.366

Gnomad OTH exome

AF:

0.354

GnomAD4 exome

AF:

0.352

AC:

502310

AN:

1428558

Hom.:

92111

Cov.:

AF XY:

0.349

AC XY:

247565

AN XY:

709180

show subpopulations

Gnomad4 AFR exome

AF:

0.0536

Gnomad4 AMR exome

AF:

0.384

Gnomad4 ASJ exome

AF:

0.431

Gnomad4 EAS exome

AF:

0.0937

Gnomad4 SAS exome

AF:

0.262

Gnomad4 FIN exome

AF:

0.371

Gnomad4 NFE exome

AF:

0.373

Gnomad4 OTH exome

AF:

0.338

GnomAD4 genome

AF:

0.274

AC:

41736

AN:

152076

Hom.:

7329

Cov.:

AF XY:

0.276

AC XY:

20554

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.0681

Gnomad4 AMR

AF:

0.348

Gnomad4 ASJ

AF:

0.430

Gnomad4 EAS

AF:

0.100

Gnomad4 SAS

AF:

0.265

Gnomad4 FIN

AF:

0.376

Gnomad4 NFE

AF:

0.372

Gnomad4 OTH

AF:

0.295

Alfa

AF:

0.283

Hom.:

1287

Bravo

AF:

0.262

Asia WGS

AF:

0.181

AC:

633

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

7.2

DANN

Benign

0.41

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