rs11874712

Variant names:

• chr18-46108610-C-A
• rs11874712
• NM_138443.4:c.205+3242C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138443.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAUS1	NM_138443.4	MANE Select	c.205+3242C>A		intron	N/A	NP_612452.1	Q96CS2-1
	HAUS1	NR_026978.2		n.272+3202C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAUS1	ENST00000282058.11	TSL:1 MANE Select	c.205+3242C>A		intron	N/A	ENSP00000282058.5	Q96CS2-1
	HAUS1	ENST00000591715.5	TSL:1	n.*2+3202C>A		intron	N/A	ENSP00000465093.1	K7EJA9
	HAUS1	ENST00000921200.1		c.205+3242C>A		intron	N/A	ENSP00000591259.1

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

African (AFR) AF: 0.224 AC: 9272 AN: 41452

American (AMR) AF: 0.285 AC: 4341 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1534 AN: 3468

East Asian (EAS) AF: 0.0481 AC: 249 AN: 5180

South Asian (SAS) AF: 0.429 AC: 2071 AN: 4828

European-Finnish (FIN) AF: 0.362 AC: 3813 AN: 10538

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28545 AN: 67966

Other (OTH) AF: 0.373 AC: 786 AN: 2106

Alfa AF: 0.371 Hom.: 4244

Bravo AF: 0.318

Asia WGS AF: 0.232 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.41
PhyloP100		0.12
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: rs11874712; hg19: chr18-43688576;