NM_001042610.3:c.31+1158G>A

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DBNDD1	NM_001042610.3	c.31+1158G>A		intron_variant	Intron 1 of 3	ENST00000002501.11	NP_001036075.1
DBNDD1	NM_001288708.2	c.-83+1575G>A		intron_variant	Intron 1 of 4		NP_001275637.1
DBNDD1	NM_001288709.2	c.-216+1575G>A		intron_variant	Intron 1 of 3		NP_001275638.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DBNDD1	ENST00000002501.11	c.31+1158G>A		intron_variant	Intron 1 of 3	2	NM_001042610.3	ENSP00000002501.6
DBNDD1	ENST00000568838.2	c.-216+1575G>A		intron_variant	Intron 1 of 3	2		ENSP00000457625.2
DBNDD1	ENST00000568330.2	n.151+1575G>A		intron_variant	Intron 1 of 4	5		ENSP00000456573.1

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

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.305

Alfa AF: 0.314 Hom.: 12970

Bravo AF: 0.264

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.0
DANN	Benign	0.38

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: rs11648785; hg19: chr16-90084561;