chr7-14922183-T-C

Variant names:

• chr7-14922183-T-C
• rs10487787
• NM_001350707.2:c.-188+52513A>G

Variant summary

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

The NM_001350707.2(DGKB):​c.-188+52513A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 152,076 control chromosomes in the GnomAD database, including 1,592 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 0.081 (1592 hom., cov: 32)
• Consequence: DGKB NM_001350707.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 4 publications found

Genes affected

DGKB (HGNC:2850): (diacylglycerol kinase beta) Diacylglycerol kinases (DGKs) are regulators of the intracellular concentration of the second messenger diacylglycerol (DAG) and thus play a key role in cellular processes. Nine mammalian isotypes have been identified, which are encoded by separate genes. Mammalian DGK isozymes contain a conserved catalytic (kinase) domain and a cysteine-rich domain (CRD). The protein encoded by this gene is a diacylglycerol kinase, beta isotype. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKB	NM_001350707.2	c.-188+52513A>G		intron_variant	Intron 1 of 25		NP_001337636.1
DGKB	NM_001350711.2	c.-188+52513A>G		intron_variant	Intron 1 of 24		NP_001337640.1
DGKB	NM_001350717.2	c.-188+52513A>G		intron_variant	Intron 1 of 24		NP_001337646.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKB	ENST00000437998.1	c.-188+52513A>G		intron_variant	Intron 1 of 4	4		ENSP00000405569.1

Frequencies

GnomAD3 genomes AF: 0.0808 AC: 12285 AN: 151958 Hom.: 1585 Cov.: 32

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0899

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0502

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.0809 AC: 12309 AN: 152076 Hom.: 1592 Cov.: 32 AF XY: 0.0904 AC XY: 6717 AN XY: 74310

African (AFR) AF: 0.0212 AC: 882 AN: 41520

American (AMR) AF: 0.0903 AC: 1379 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3466

East Asian (EAS) AF: 0.638 AC: 3283 AN: 5144

South Asian (SAS) AF: 0.323 AC: 1553 AN: 4814

European-Finnish (FIN) AF: 0.103 AC: 1093 AN: 10578

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0502 AC: 3412 AN: 67960

Other (OTH) AF: 0.0833 AC: 176 AN: 2114

Alfa AF: 0.0566 Hom.: 96

Bravo AF: 0.0770

Asia WGS AF: 0.431 AC: 1495 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.7
DANN	Benign	0.47
PhyloP100		0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10487787; hg19: chr7-14961808;