Variant rs17132382 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000443786.3(HAUS3):c.1578+1756G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 153,362 control chromosomes in the GnomAD database, including 3,617 homozygotes. 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 0.17 ( 3600 hom., cov: 32)

Exomes 𝑓: 0.12 ( 17 hom. )

Consequence

HAUS3
ENST00000443786.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.709

Variant links:

Genes affected

HAUS3 (HGNC:28719): (HAUS augmin like complex subunit 3) This gene encodes a component of the HAUS augmin-like protein complex, which plays a key role in cytokinesis and mitosis. Disruption of the encoded protein causes mitotic defects resulting from fragmentation of centrosomes and microtubule destabilization. This gene shares its 5' exons with some transcripts from overlapping GeneID: 353497, which encodes a DNA polymerase. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

HAUS3 links:

POLN (HGNC:18870): (DNA polymerase nu) This gene encodes a DNA polymerase type-A family member. The encoded protein plays a role in DNA repair and homologous recombination. This gene shares its 5' exons with some transcripts from overlapping GeneID: 79441, which encodes an augmentin-like protein complex subunit. [provided by RefSeq, Dec 2014]

POLN links:

COX6B1P5 (HGNC:37675): (cytochrome c oxidase subunit 6B1 pseudogene 5)

COX6B1P5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
HAUS3	NM_001303143.2 linkuse as main transcript	c.1578+1756G>A	intron_variant	ENST00000443786.3	NP_001290072.1
POLN	NM_181808.4 linkuse as main transcript	c.-12-5229G>A	intron_variant	ENST00000511885.6	NP_861524.2
HAUS3	NM_024511.7 linkuse as main transcript	c.1578+1756G>A	intron_variant		NP_078787.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HAUS3	ENST00000443786.3 linkuse as main transcript	c.1578+1756G>A	intron_variant		1	NM_001303143.2	ENSP00000392903	P1	Q68CZ6-1
POLN	ENST00000511885.6 linkuse as main transcript	c.-12-5229G>A	intron_variant		5	NM_181808.4	ENSP00000435506	P1	Q7Z5Q5-1
COX6B1P5	ENST00000509843.2 linkuse as main transcript	n.222C>T	non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25218

AN:

151984

Hom.:

3590

Cov.:

show subpopulations

Gnomad AFR

AF:

0.367

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.170

Gnomad ASJ

AF:

0.0749

Gnomad EAS

AF:

0.349

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.0302

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0584

Gnomad OTH

AF:

0.174

GnomAD4 exome

AF:

0.115

AC:

145

AN:

1258

Hom.:

Cov.:

AF XY:

0.108

AC XY:

AN XY:

720

show subpopulations

Gnomad4 AFR exome

AF:

0.386

Gnomad4 AMR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.375

Gnomad4 SAS exome

AF:

0.125

Gnomad4 FIN exome

AF:

0.0463

Gnomad4 NFE exome

AF:

0.0539

Gnomad4 OTH exome

AF:

0.217

GnomAD4 genome

AF:

0.166

AC:

25263

AN:

152104

Hom.:

3600

Cov.:

AF XY:

0.165

AC XY:

12250

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.367

Gnomad4 AMR

AF:

0.170

Gnomad4 ASJ

AF:

0.0749

Gnomad4 EAS

AF:

0.348

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.0302

Gnomad4 NFE

AF:

0.0584

Gnomad4 OTH

AF:

0.176

Alfa

AF:

0.123

Hom.:

335

Bravo

AF:

0.191

Asia WGS

AF:

0.272

AC:

947

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

2.0

DANN

Benign

0.68

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over