rs11874712

chr18-46108610-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138443.4(HAUS1):c.205+3242C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,974 control chromosomes in the GnomAD database, including 9,383 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 0.34 (9383 hom., cov: 31)
• Consequence: HAUS1 NM_138443.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

Genes affected

HAUS1 (HGNC:25174): (HAUS augmin like complex subunit 1) HAUS1 is 1 of 8 subunits of the 390-kD human augmin complex, or HAUS complex. The augmin complex was first identified in Drosophila, and its name comes from the Latin verb 'augmentare,' meaning 'to increase.' The augmin complex is a microtubule-binding complex involved in microtubule generation within the mitotic spindle and is vital to mitotic spindle assembly (Goshima et al., 2008 [PubMed 18443220]; Uehara et al., 2009 [PubMed 19369198]).[supplied by OMIM, Jun 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HAUS1	NM_138443.4	c.205+3242C>A		intron_variant		ENST00000282058.11
HAUS1	NR_026978.2	n.272+3202C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HAUS1	ENST00000282058.11	c.205+3242C>A		intron_variant		1	NM_138443.4	P1

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51128 AN: 151856 Hom.: 9390 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.0482

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.336 AC: 51119 AN: 151974 Hom.: 9383 Cov.: 31 AF XY: 0.333 AC XY: 24753 AN XY: 74286

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.0481

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.373

Alfa AF: 0.369 Hom.: 3353

Bravo AF: 0.318

Asia WGS AF: 0.232 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.6
Dann	Benign	0.41

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

Other links and lift over

dbSNP: rs11874712; hg19: chr18-43688576;