chr7-6408901-T-C

Variant names:

• chr7-6408901-T-C
• rs3813517
• NM_139179.4:c.*936A>G

Variant summary

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

The NM_139179.4(DAGLB):​c.*936A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0273 in 152,254 control chromosomes in the GnomAD database, including 91 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 0.027 (91 hom., cov: 32)
• Consequence: DAGLB NM_139179.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 7 publications found

Genes affected

DAGLB (HGNC:28923): (diacylglycerol lipase beta) Enables lipase activity. Involved in arachidonic acid metabolic process. Located in nucleoplasm and plasma membrane. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAGLB	NM_139179.4	c.*936A>G		downstream_gene_variant		ENST00000297056.11	NP_631918.3
DAGLB	NM_001142936.2	c.*936A>G		downstream_gene_variant			NP_001136408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAGLB	ENST00000297056.11	c.*936A>G		downstream_gene_variant		1	NM_139179.4	ENSP00000297056.6
DAGLB	ENST00000462934.5	n.*225A>G		downstream_gene_variant		2
DAGLB	ENST00000482149.5	n.*229A>G		downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.0272 AC: 4143 AN: 152136 Hom.: 91 Cov.: 32

Gnomad AFR AF: 0.0288

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0185

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.00828

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0205

Gnomad OTH AF: 0.0273

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

GnomAD4 genome AF: 0.0273 AC: 4151 AN: 152254 Hom.: 91 Cov.: 32 AF XY: 0.0286 AC XY: 2127 AN XY: 74440

African (AFR) AF: 0.0289 AC: 1202 AN: 41540

American (AMR) AF: 0.0188 AC: 288 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3466

East Asian (EAS) AF: 0.0931 AC: 481 AN: 5166

South Asian (SAS) AF: 0.0980 AC: 472 AN: 4814

European-Finnish (FIN) AF: 0.00828 AC: 88 AN: 10628

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0205 AC: 1395 AN: 68032

Other (OTH) AF: 0.0265 AC: 56 AN: 2112

Alfa AF: 0.0221 Hom.: 10

Bravo AF: 0.0265

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.38
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3813517; hg19: chr7-6448532;