NM_181645.4:c.1639-3978T>G

Variant names:

• chr11-93433565-T-G
• rs2658782
• NM_181645.4:c.1639-3978T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181645.4(DEUP1):​c.1639-3978T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 152,132 control chromosomes in the GnomAD database, including 52,614 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 0.83 (52614 hom., cov: 31)
• Consequence: DEUP1 NM_181645.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.868
• Publications: 7 publications found

Genes affected

DEUP1 (HGNC:26344): (deuterosome assembly protein 1) Enables identical protein binding activity. Predicted to be involved in centriole replication and de novo centriole assembly involved in multi-ciliated epithelial cell differentiation. Predicted to be located in cytoplasm. Predicted to be integral component of membrane. Predicted to be active in centriole and deuterosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181645.4. 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
	DEUP1	NM_181645.4	MANE Select	c.1639-3978T>G		intron	N/A	NP_857596.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DEUP1	ENST00000298050.9	TSL:5 MANE Select	c.1639-3978T>G		intron	N/A	ENSP00000298050.3
	DEUP1	ENST00000525646.1	TSL:1	c.865-3978T>G		intron	N/A	ENSP00000435079.1
	DEUP1	ENST00000529909.1	TSL:3	n.280-3978T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126283 AN: 152014 Hom.: 52565 Cov.: 31

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.831 AC: 126389 AN: 152132 Hom.: 52614 Cov.: 31 AF XY: 0.836 AC XY: 62172 AN XY: 74382

African (AFR) AF: 0.850 AC: 35272 AN: 41486

American (AMR) AF: 0.864 AC: 13208 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2743 AN: 3470

East Asian (EAS) AF: 0.912 AC: 4720 AN: 5176

South Asian (SAS) AF: 0.883 AC: 4251 AN: 4812

European-Finnish (FIN) AF: 0.851 AC: 9014 AN: 10594

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.800 AC: 54417 AN: 67988

Other (OTH) AF: 0.823 AC: 1740 AN: 2114

Alfa AF: 0.815 Hom.: 53053

Bravo AF: 0.834

Asia WGS AF: 0.898 AC: 3120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.36
PhyloP100		-0.87
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: rs2658782; hg19: chr11-93166731;