X-153454511-GGGGAGGGAGGGAGGGAGGGAGGGA-GGGGAGGGA

Variant names:

• chrX-153454511-GGGGAGGGAGGGAGGGA-G
• rs371637396
• NM_001385482.1:c.931-19_931-4delTCCCTCCCTCCCTCCC

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6 BS2

The NM_001385482.1(HAUS7):​c.931-19_931-4delTCCCTCCCTCCCTCCC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000179 in 569,133 control chromosomes in the GnomAD database, including 2 homozygotes. There are 35 hemizygotes in GnomAD. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.00031 (0 hom., 3 hem., cov: 0)
  • Exomes 𝑓: 0.00016 (2 hom. 32 hem.)
• Consequence: HAUS7 NM_001385482.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• 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 -5 ACMG points.

• BP6: Variant X-153454511-GGGGAGGGAGGGAGGGA-G is Benign according to our data. Variant chrX-153454511-GGGGAGGGAGGGAGGGA-G is described in Lovd as [Likely_benign].
• BS2: High Hemizygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAUS7	NM_001385482.1	c.931-19_931-4delTCCCTCCCTCCCTCCC		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.931-19_931-4delTCCCTCCCTCCCTCCC		splice_region_variant, intron_variant	Intron 8 of 9	1	NM_001385482.1	ENSP00000359230.6

Frequencies

GnomAD3 genomes AF: 0.000311 AC: 26 AN: 83693 Hom.: 0 Cov.: 0 AF XY: 0.000161 AC XY: 3 AN XY: 18681

Gnomad AFR AF: 0.000579

Gnomad AMI AF: 0.00387

Gnomad AMR AF: 0.000293

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000224

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000304 AC: 25 AN: 82269 Hom.: 2 AF XY: 0.000430 AC XY: 8 AN XY: 18595

Gnomad AFR exome AF: 0.000315

Gnomad AMR exome AF: 0.000150

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000547

Gnomad SAS exome AF: 0.000589

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000369

Gnomad OTH exome AF: 0.000416

GnomAD4 exome AF: 0.000157 AC: 76 AN: 485431 Hom.: 2 AF XY: 0.000257 AC XY: 32 AN XY: 124531

Gnomad4 AFR exome AF: 0.000225

Gnomad4 AMR exome AF: 0.000155

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000290

Gnomad4 SAS exome AF: 0.000322

Gnomad4 FIN exome AF: 0.0000336

Gnomad4 NFE exome AF: 0.000145

Gnomad4 OTH exome AF: 0.000215

GnomAD4 genome AF: 0.000311 AC: 26 AN: 83702 Hom.: 0 Cov.: 0 AF XY: 0.000160 AC XY: 3 AN XY: 18712

Gnomad4 AFR AF: 0.000578

Gnomad4 AMR AF: 0.000292

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000225

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

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;