NM_001385482.1:c.931-15_931-4delTCCCTCCCTCCC

Variant names:

• chrX-153454511-GGGGAGGGAGGGA-G
• rs371637396
• NM_001385482.1:c.931-15_931-4delTCCCTCCCTCCC

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_001385482.1(HAUS7):​c.931-15_931-4delTCCCTCCCTCCC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00113 in 569,105 control chromosomes in the GnomAD database, including 10 homozygotes. There are 158 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0021 (5 hom., 27 hem., cov: 0)
  • Exomes 𝑓: 0.00096 (5 hom. 131 hem.)
• Consequence: HAUS7 NM_001385482.1 splice_region, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.589

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]

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]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant X-153454511-GGGGAGGGAGGGA-G is Benign according to our data. Variant chrX-153454511-GGGGAGGGAGGGA-G is described in ClinVar as [Likely_benign]. Clinvar id is 782830.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAUS7	NM_001385482.1	c.931-15_931-4delTCCCTCCCTCCC		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	c.931-15_931-4delTCCCTCCCTCCC		splice_region_variant, intron_variant	Intron 8 of 9	1	NM_001385482.1	ENSP00000359230.6

Frequencies

GnomAD3 genomes AF: 0.00211 AC: 177 AN: 83689 Hom.: 5 Cov.: 0 AF XY: 0.00145 AC XY: 27 AN XY: 18679

Gnomad AFR AF: 0.000917

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.00571

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0216

Gnomad NFE AF: 0.00130

Gnomad OTH AF: 0.00477

GnomAD3 exomes AF: 0.00148 AC: 122 AN: 82269 Hom.: 8 AF XY: 0.00199 AC XY: 37 AN XY: 18595

Gnomad AFR exome AF: 0.00110

Gnomad AMR exome AF: 0.00105

Gnomad ASJ exome AF: 0.00504

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000294

Gnomad FIN exome AF: 0.000371

Gnomad NFE exome AF: 0.00190

Gnomad OTH exome AF: 0.00250

GnomAD4 exome AF: 0.000964 AC: 468 AN: 485407 Hom.: 5 AF XY: 0.00105 AC XY: 131 AN XY: 124515

Gnomad4 AFR exome AF: 0.000600

Gnomad4 AMR exome AF: 0.00160

Gnomad4 ASJ exome AF: 0.00464

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000225

Gnomad4 FIN exome AF: 0.000639

Gnomad4 NFE exome AF: 0.000825

Gnomad4 OTH exome AF: 0.00240

GnomAD4 genome AF: 0.00211 AC: 177 AN: 83698 Hom.: 5 Cov.: 0 AF XY: 0.00144 AC XY: 27 AN XY: 18710

Gnomad4 AFR AF: 0.000916

Gnomad4 AMR AF: 0.00570

Gnomad4 ASJ AF: 0.00576

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00130

Gnomad4 OTH AF: 0.00470

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Dec 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs371637396; hg19: chrX-152719969;