X-153464618-G-A

Variant names:

• chrX-153464618-G-A
• rs933190
• NM_001385482.1:c.292+370C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001385482.1(HAUS7):​c.292+370C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.53 (12017 hom., 17894 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: HAUS7 NM_001385482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 4 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAUS7	NM_001385482.1	c.292+370C>T		intron_variant	Intron 3 of 9	ENST00000370211.10	NP_001372411.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAUS7	ENST00000370211.10	c.292+370C>T		intron_variant	Intron 3 of 9	1	NM_001385482.1	ENSP00000359230.6

Frequencies

GnomAD3 genomes AF: 0.534 AC: 59492 AN: 111471 Hom.: 12017 Cov.: 24

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.641

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.551

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.534 AC: 59509 AN: 111526 Hom.: 12017 Cov.: 24 AF XY: 0.530 AC XY: 17894 AN XY: 33758

African (AFR) AF: 0.333 AC: 10226 AN: 30716

American (AMR) AF: 0.593 AC: 6300 AN: 10619

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 1775 AN: 2646

East Asian (EAS) AF: 0.327 AC: 1149 AN: 3519

South Asian (SAS) AF: 0.294 AC: 795 AN: 2700

European-Finnish (FIN) AF: 0.651 AC: 3892 AN: 5976

Middle Eastern (MID) AF: 0.644 AC: 139 AN: 216

European-Non Finnish (NFE) AF: 0.641 AC: 33956 AN: 52947

Other (OTH) AF: 0.556 AC: 840 AN: 1510

Alfa AF: 0.572 Hom.: 22556

Bravo AF: 0.529

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.60
PhyloP100		0.076
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs933190; hg19: chrX-152730076;