chr15-89101707-G-A

Variant names:

• chr15-89101707-G-A
• rs293381
• NM_152924.5:c.-106-12018G>A

Variant summary

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

The NM_152924.5(ABHD2):​c.-106-12018G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 152,056 control chromosomes in the GnomAD database, including 18,998 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 0.48 (18998 hom., cov: 32)
• Consequence: ABHD2 NM_152924.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

ABHD2 (HGNC:18717): (abhydrolase domain containing 2, acylglycerol lipase) This gene encodes a protein containing an alpha/beta hydrolase fold, which is a catalytic domain found in a wide range of enzymes. The encoded protein is an acylglycerol lipase that catalyzes the hydrolysis of endocannabinoid arachidonoylglycerol from the cell membrane. This leads to activation of the sperm calcium channel CatSper, which results in sperm activation. Alternative splicing of this gene results in two transcript variants encoding the same protein. [provided by RefSeq, Jan 2017]

LOC124903573 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABHD2	NM_152924.5	c.-106-12018G>A		intron_variant	Intron 1 of 10	ENST00000352732.10	NP_690888.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABHD2	ENST00000352732.10	c.-106-12018G>A		intron_variant	Intron 1 of 10	1	NM_152924.5	ENSP00000268129.5

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72447 AN: 151938 Hom.: 18956 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.477 AC: 72543 AN: 152056 Hom.: 18998 Cov.: 32 AF XY: 0.467 AC XY: 34710 AN XY: 74338

African (AFR) AF: 0.695 AC: 28806 AN: 41462

American (AMR) AF: 0.333 AC: 5088 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1072 AN: 3462

East Asian (EAS) AF: 0.188 AC: 972 AN: 5184

South Asian (SAS) AF: 0.384 AC: 1852 AN: 4826

European-Finnish (FIN) AF: 0.390 AC: 4118 AN: 10562

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29292 AN: 67976

Other (OTH) AF: 0.433 AC: 914 AN: 2112

Alfa AF: 0.453 Hom.: 6623

Bravo AF: 0.482

Asia WGS AF: 0.346 AC: 1203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.054
DANN	Benign	0.51
PhyloP100		-1.4
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

Publications

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Other links and lift over

dbSNP: rs293381; hg19: chr15-89644938;