rs8059973

Positions:

• chr16-90013126-A-G
• chr16-90013126-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001042610.3(DBNDD1):​c.32-3696T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 151,264 control chromosomes in the GnomAD database, including 45,844 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 0.77 (45844 hom., cov: 27)
• Consequence: DBNDD1 NM_001042610.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574

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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DBNDD1	NM_001042610.3	c.32-3696T>C		intron_variant		ENST00000002501.11
DBNDD1	NM_001288708.2	c.-82-1430T>C		intron_variant
DBNDD1	NM_001288709.2	c.-215-3696T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DBNDD1	ENST00000002501.11	c.32-3696T>C		intron_variant		2	NM_001042610.3	P1
DBNDD1	ENST00000568838.2	c.-215-3696T>C		intron_variant		2
DBNDD1	ENST00000568330.2	c.154-1430T>C		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.772 AC: 116755 AN: 151148 Hom.: 45826 Cov.: 27

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.772 AC: 116817 AN: 151264 Hom.: 45844 Cov.: 27 AF XY: 0.763 AC XY: 56320 AN XY: 73838

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.846

Gnomad4 OTH AF: 0.763

Alfa AF: 0.829 Hom.: 73752

Bravo AF: 0.765

Asia WGS AF: 0.614 AC: 2132 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.9
DANN	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs8059973; hg19: chr16-90079534;