16-90018153-C-T

Variant names:

• chr16-90018153-C-T
• rs11648785
• NM_001042610.3:c.31+1158G>A

Variant summary

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

The NM_001042610.3(DBNDD1):​c.31+1158G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,114 control chromosomes in the GnomAD database, including 6,014 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 0.27 (6014 hom., cov: 33)
• Consequence: DBNDD1 NM_001042610.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 36 publications found

Genes affected

DBNDD1 (HGNC:28455): (dysbindin domain containing 1) Predicted to be involved in negative regulation of protein kinase activity. Predicted to be located in cytoplasm. [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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001042610.3. 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
	DBNDD1	NM_001042610.3	MANE Select	c.31+1158G>A		intron	N/A	NP_001036075.1	Q9H9R9-1
	DBNDD1	NM_001288708.2		c.-83+1575G>A		intron	N/A	NP_001275637.1
	DBNDD1	NM_001288709.2		c.-216+1575G>A		intron	N/A	NP_001275638.2	D3DX86

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DBNDD1	ENST00000002501.11	TSL:2 MANE Select	c.31+1158G>A		intron	N/A	ENSP00000002501.6	Q9H9R9-1
	DBNDD1	ENST00000930202.1		c.31+1158G>A		intron	N/A	ENSP00000600261.1
	DBNDD1	ENST00000930203.1		c.31+1158G>A		intron	N/A	ENSP00000600262.1

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41180 AN: 151994 Hom.: 6008 Cov.: 33

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.271 AC: 41205 AN: 152114 Hom.: 6014 Cov.: 33 AF XY: 0.271 AC XY: 20145 AN XY: 74352

African (AFR) AF: 0.169 AC: 7032 AN: 41494

American (AMR) AF: 0.306 AC: 4673 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 736 AN: 3470

East Asian (EAS) AF: 0.182 AC: 942 AN: 5166

South Asian (SAS) AF: 0.429 AC: 2070 AN: 4824

European-Finnish (FIN) AF: 0.265 AC: 2807 AN: 10584

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21862 AN: 67966

Other (OTH) AF: 0.305 AC: 645 AN: 2112

Alfa AF: 0.300 Hom.: 25797

Bravo AF: 0.264

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.0
DANN	Benign	0.38
PhyloP100		0.043
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: rs11648785; hg19: chr16-90084561;