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

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_001385482.1(HAUS7):c.931-7_931-4dupTCCC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.013 ( 13 hom., 44 hem., cov: 0)

Exomes 𝑓: 0.0048 ( 8 hom. 333 hem. )

Consequence

HAUS7
NM_001385482.1 splice_region, intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.452

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 Benign. Variant got -10 ACMG points.

BP6

Variant X-153454511-G-GGGGA is Benign according to our data. Variant chrX-153454511-G-GGGGA is described in ClinVar as [Likely_benign]. Clinvar id is 779001.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0132 (1106/83670) while in subpopulation AFR AF= 0.0273 (566/20726). AF 95% confidence interval is 0.0254. There are 13 homozygotes in gnomad4. There are 44 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 13 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAUS7	NM_001385482.1 link	c.931-7_931-4dupTCCC		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.931-7_931-4dupTCCC		splice_region_variant, intron_variant	Intron 8 of 9	1	NM_001385482.1	ENSP00000359230.6		Q99871-1

Frequencies

GnomAD3 genomes

AF:

0.0132

AC:

1107

AN:

83661

Hom.:

Cov.:

AF XY:

0.00236

AC XY:

AN XY:

18679

show subpopulations

Gnomad AFR

AF:

0.0274

Gnomad AMI

AF:

0.00774

Gnomad AMR

AF:

0.00717

Gnomad ASJ

AF:

0.0146

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000814

Gnomad FIN

AF:

0.00649

Gnomad MID

AF:

0.00541

Gnomad NFE

AF:

0.00932

Gnomad OTH

AF:

0.00954

GnomAD3 exomes

AF:

0.00349

AC:

287

AN:

82269

Hom.:

AF XY:

0.000807

AC XY:

AN XY:

18595

show subpopulations

Gnomad AFR exome

AF:

0.0180

Gnomad AMR exome

AF:

0.00277

Gnomad ASJ exome

AF:

0.00329

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000883

Gnomad FIN exome

AF:

0.000619

Gnomad NFE exome

AF:

0.00298

Gnomad OTH exome

AF:

0.00208

GnomAD4 exome

AF:

0.00483

AC:

2343

AN:

485048

Hom.:

Cov.:

AF XY:

0.00268

AC XY:

333

AN XY:

124220

show subpopulations

Gnomad4 AFR exome

AF:

0.0171

Gnomad4 AMR exome

AF:

0.00331

Gnomad4 ASJ exome

AF:

0.00692

Gnomad4 EAS exome

AF:

0.000116

Gnomad4 SAS exome

AF:

0.00138

Gnomad4 FIN exome

AF:

0.00505

Gnomad4 NFE exome

AF:

0.00477

Gnomad4 OTH exome

AF:

0.00679

GnomAD4 genome

AF:

0.0132

AC:

1106

AN:

83670

Hom.:

Cov.:

AF XY:

0.00235

AC XY:

AN XY:

18710

show subpopulations

Gnomad4 AFR

AF:

0.0273

Gnomad4 AMR

AF:

0.00716

Gnomad4 ASJ

AF:

0.0146

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000820

Gnomad4 FIN

AF:

0.00649

Gnomad4 NFE

AF:

0.00932

Gnomad4 OTH

AF:

0.00940

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Oct 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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