chr11-93433565-T-G

Position:

• chr11-93433565-T-G

Variant summary

Our verdict is Benign. Variant got -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

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]

DEUP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DEUP1	NM_181645.4	c.1639-3978T>G		intron_variant		ENST00000298050.9	NP_857596.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DEUP1	ENST00000298050.9	c.1639-3978T>G		intron_variant		5	NM_181645.4	ENSP00000298050.3

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

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.851

Gnomad4 NFE AF: 0.800

Gnomad4 OTH AF: 0.823

Alfa AF: 0.805 Hom.: 26381

Bravo AF: 0.834

Asia WGS AF: 0.898 AC: 3120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.36

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: rs2658782; hg19: chr11-93166731;