rs371637396

Variant names:

• chrX-153454511-GGGGAGGGAGGGAGGGAGGGAGGGA-G
• rs371637396
• NM_001385482.1:c.931-27_931-4delTCCCTCCCTCCCTCCCTCCCTCCC

Your query was ambiguous. Multiple possible variants found:

• chrX-153454511-GGGGAGGGAGGGAGGGAGGGAGGGA-G
• chrX-153454511-GGGGAGGGAGGGAGGGAGGGAGGGA-GGGGA
• chrX-153454511-GGGGAGGGAGGGAGGGAGGGAGGGA-GGGGAGGGA
• chrX-153454511-GGGGAGGGAGGGAGGGAGGGAGGGA-GGGGAGGGAGGGA
• chrX-153454511-GGGGAGGGAGGGAGGGAGGGAGGGA-GGGGAGGGAGGGAGGGA
• chrX-153454511-GGGGAGGGAGGGAGGGAGGGAGGGA-GGGGAGGGAGGGAGGGAGGGA
• chrX-153454511-GGGGAGGGAGGGAGGGAGGGAGGGA-GGGGAGGGAGGGAGGGAGGGAGGGAGGGA
• chrX-153454511-GGGGAGGGAGGGAGGGAGGGAGGGA-GGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA
• chrX-153454511-GGGGAGGGAGGGAGGGAGGGAGGGA-GGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA
• chrX-153454511-GGGGAGGGAGGGAGGGAGGGAGGGA-GGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001385482.1(HAUS7):​c.931-27_931-4delTCCCTCCCTCCCTCCCTCCCTCCC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000144 in 485,462 control chromosomes in the GnomAD database, including 1 homozygotes. There are no hemizygote samples in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.000014 (1 hom. 0 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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAUS7	NM_001385482.1	c.931-27_931-4delTCCCTCCCTCCCTCCCTCCCTCCC		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.931-27_931-4delTCCCTCCCTCCCTCCCTCCCTCCC		splice_region_variant, intron_variant	Intron 8 of 9	1	NM_001385482.1	ENSP00000359230.6

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.0000144 AC: 7 AN: 485462 Hom.: 1 AF XY: 0.00 AC XY: 0 AN XY: 124552

Gnomad4 AFR exome AF: 0.000150

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000321

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000119

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

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;