X-153454511-GGGGAGGGAGGGAGGGAGGGAGGGA-GGGGAGGGAGGGAGGGAGGGA

Variant names:

• chrX-153454511-GGGGA-G
• rs371637396
• NM_001385482.1:c.931-7_931-4delTCCC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001385482.1(HAUS7):​c.931-7_931-4delTCCC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 556,691 control chromosomes in the GnomAD database, including 18,946 homozygotes. There are 29,541 hemizygotes in GnomAD. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.30 (5031 hom., 2438 hem., cov: 0)
  • Exomes 𝑓: 0.19 (13915 hom. 27103 hem.)
• Consequence: HAUS7 NM_001385482.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.303 AC: 25317 AN: 83548 Hom.: 5034 Cov.: 0 AF XY: 0.130 AC XY: 2429 AN XY: 18644

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.195

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.305

GnomAD3 exomes AF: 0.178 AC: 14639 AN: 82269 Hom.: 3439 AF XY: 0.159 AC XY: 2954 AN XY: 18595

Gnomad AFR exome AF: 0.192

Gnomad AMR exome AF: 0.212

Gnomad ASJ exome AF: 0.0515

Gnomad EAS exome AF: 0.608

Gnomad SAS exome AF: 0.287

Gnomad FIN exome AF: 0.105

Gnomad NFE exome AF: 0.108

Gnomad OTH exome AF: 0.172

GnomAD4 exome AF: 0.195 AC: 92147 AN: 473134 Hom.: 13915 AF XY: 0.228 AC XY: 27103 AN XY: 118726

Gnomad4 AFR exome AF: 0.185

Gnomad4 AMR exome AF: 0.270

Gnomad4 ASJ exome AF: 0.142

Gnomad4 EAS exome AF: 0.761

Gnomad4 SAS exome AF: 0.511

Gnomad4 FIN exome AF: 0.226

Gnomad4 NFE exome AF: 0.131

Gnomad4 OTH exome AF: 0.218

GnomAD4 genome AF: 0.303 AC: 25315 AN: 83557 Hom.: 5031 Cov.: 0 AF XY: 0.131 AC XY: 2438 AN XY: 18675

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.909

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs371637396; hg19: chrX-152719969;