3-58284024-G-T

Variant names:

• chr3-58284024-G-T
• rs3773010
• NM_001320126.2:c.682-1061G>T

Variant summary

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

The NM_001320126.2(ABHD6):​c.682-1061G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,094 control chromosomes in the GnomAD database, including 6,843 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 0.30 (6843 hom., cov: 32)
• Consequence: ABHD6 NM_001320126.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 10 publications found

Genes affected

ABHD6 (HGNC:21398): (abhydrolase domain containing 6, acylglycerol lipase) Enables acylglycerol lipase activity. Involved in acylglycerol catabolic process. Predicted to be located in late endosome membrane and lysosomal membrane. Predicted to be integral component of membrane. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in GABA-ergic synapse; glutamatergic synapse; and mitochondrion. Predicted to be integral component of postsynaptic 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 (AFR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABHD6	NM_001320126.2	c.682-1061G>T		intron_variant	Intron 7 of 9	ENST00000478253.6	NP_001307055.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABHD6	ENST00000478253.6	c.682-1061G>T		intron_variant	Intron 7 of 9	2	NM_001320126.2	ENSP00000420315.1
ABHD6	ENST00000295962.8	c.682-1061G>T		intron_variant	Intron 6 of 8	1		ENSP00000295962.4

Frequencies

GnomAD3 genomes AF: 0.296 AC: 45003 AN: 151976 Hom.: 6833 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.296 AC: 45057 AN: 152094 Hom.: 6843 Cov.: 32 AF XY: 0.295 AC XY: 21935 AN XY: 74342

African (AFR) AF: 0.357 AC: 14785 AN: 41466

American (AMR) AF: 0.283 AC: 4315 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1008 AN: 3470

East Asian (EAS) AF: 0.214 AC: 1106 AN: 5174

South Asian (SAS) AF: 0.212 AC: 1021 AN: 4818

European-Finnish (FIN) AF: 0.301 AC: 3189 AN: 10602

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18801 AN: 67984

Other (OTH) AF: 0.282 AC: 595 AN: 2112

Alfa AF: 0.279 Hom.: 20189

Bravo AF: 0.299

Asia WGS AF: 0.228 AC: 796 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	3.2
DANN	Benign	0.68
PhyloP100		-0.11
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: rs3773010; hg19: chr3-58269751;