Variant X-153454511-GGGGAGGGA-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001385482.1(HAUS7):c.931-11_931-4delTCCCTCCC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00254 in 563,239 control chromosomes in the GnomAD database, including 10 homozygotes. There are 267 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0041 ( 4 hom., 56 hem., cov: 0)

Exomes 𝑓: 0.0023 ( 6 hom. 211 hem. )

Consequence

HAUS7
NM_001385482.1 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.589

Variant links:

Genes affected

HAUS7 (HGNC:32979): (HAUS augmin like complex subunit 7) This gene encodes a subunit of the augmin complex, which regulates centrosome and mitotic spindle integrity, and is necessary for the completion of cytokinesis. The encoded protein was identified by interaction with ubiquitin C-terminal hydrolase 37. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2012]

HAUS7 links:

TREX2 (HGNC:12270): (three prime repair exonuclease 2) This gene encodes a nuclear protein with 3' to 5' exonuclease activity. The encoded protein participates in double-stranded DNA break repair, and may interact with DNA polymerase delta. [provided by RefSeq, Nov 2012]

TREX2 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant X-153454511-GGGGAGGGA-G is Benign according to our data. Variant chrX-153454511-GGGGAGGGA-G is described in ClinVar as [Benign]. Clinvar id is 712156.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAUS7	NM_001385482.1 link	c.931-11_931-4delTCCCTCCC		splice_region_variant, intron_variant	Intron 8 of 9	ENST00000370211.10	NP_001372411.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAUS7	ENST00000370211.10 link	c.931-11_931-4delTCCCTCCC		splice_region_variant, intron_variant	Intron 8 of 9	1	NM_001385482.1	ENSP00000359230.6		Q99871-1

Frequencies

GnomAD3 genomes

AF:

0.00409

AC:

342

AN:

83682

Hom.:

Cov.:

AF XY:

0.00294

AC XY:

AN XY:

18676

show subpopulations

Gnomad AFR

AF:

0.0115

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00351

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00181

Gnomad SAS

AF:

0.00163

Gnomad FIN

AF:

0.000240

Gnomad MID

AF:

0.00541

Gnomad NFE

AF:

0.00148

Gnomad OTH

AF:

0.00477

GnomAD3 exomes

AF:

0.00329

AC:

271

AN:

82269

Hom.:

AF XY:

0.00183

AC XY:

AN XY:

18595

show subpopulations

Gnomad AFR exome

AF:

0.0113

Gnomad AMR exome

AF:

0.00180

Gnomad ASJ exome

AF:

0.000876

Gnomad EAS exome

AF:

0.00712

Gnomad SAS exome

AF:

0.00442

Gnomad FIN exome

AF:

0.00309

Gnomad NFE exome

AF:

0.00202

Gnomad OTH exome

AF:

0.00250

GnomAD4 exome

AF:

0.00226

AC:

1086

AN:

479548

Hom.:

AF XY:

0.00173

AC XY:

211

AN XY:

121926

show subpopulations

Gnomad4 AFR exome

AF:

0.00765

Gnomad4 AMR exome

AF:

0.00420

Gnomad4 ASJ exome

AF:

0.000790

Gnomad4 EAS exome

AF:

0.00851

Gnomad4 SAS exome

AF:

0.00497

Gnomad4 FIN exome

AF:

0.00235

Gnomad4 NFE exome

AF:

0.00137

Gnomad4 OTH exome

AF:

0.00335

GnomAD4 genome

AF:

0.00409

AC:

342

AN:

83691

Hom.:

Cov.:

AF XY:

0.00299

AC XY:

AN XY:

18707

show subpopulations

Gnomad4 AFR

AF:

0.0116

Gnomad4 AMR

AF:

0.00351

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00182

Gnomad4 SAS

AF:

0.00164

Gnomad4 FIN

AF:

0.000240

Gnomad4 NFE

AF:

0.00148

Gnomad4 OTH

AF:

0.00470

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Dec 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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