NM_001102368.3:c.-82+12674A>G

Variant names:

• chr14-91126957-A-G
• rs7146008
• NM_001102368.3:c.-82+12674A>G

Variant summary

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

The NM_001102368.3(DGLUCY):​c.-82+12674A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,416 control chromosomes in the GnomAD database, including 28,113 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 0.60 (28113 hom., cov: 29)
• Consequence: DGLUCY NM_001102368.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.850
• Publications: 12 publications found

Genes affected

DGLUCY (HGNC:20498): (D-glutamate cyclase) Predicted to enable D-glutamate cyclase activity. Predicted to be involved in glutamate metabolic process. Predicted to be located in mitochondrial matrix. [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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGLUCY	NM_001102368.3	c.-82+12674A>G		intron_variant	Intron 1 of 13	ENST00000256324.15	NP_001095838.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGLUCY	ENST00000256324.15	c.-82+12674A>G		intron_variant	Intron 1 of 13	1	NM_001102368.3	ENSP00000256324.9

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90103 AN: 151308 Hom.: 28098 Cov.: 29

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.595 AC: 90157 AN: 151416 Hom.: 28113 Cov.: 29 AF XY: 0.603 AC XY: 44583 AN XY: 73894

African (AFR) AF: 0.402 AC: 16562 AN: 41232

American (AMR) AF: 0.663 AC: 10063 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2148 AN: 3470

East Asian (EAS) AF: 0.906 AC: 4661 AN: 5142

South Asian (SAS) AF: 0.755 AC: 3624 AN: 4800

European-Finnish (FIN) AF: 0.683 AC: 7097 AN: 10392

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44002 AN: 67898

Other (OTH) AF: 0.630 AC: 1322 AN: 2100

Alfa AF: 0.636 Hom.: 136380

Bravo AF: 0.586

Asia WGS AF: 0.797 AC: 2772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.13
DANN	Benign	0.56
PhyloP100		-0.85
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: rs7146008; hg19: chr14-91593301;