rs11662721

chr18-21681452-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138340.5(ABHD3):c.555+2468G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,054 control chromosomes in the GnomAD database, including 1,983 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 0.15 (1983 hom., cov: 31)
• Consequence: ABHD3 NM_138340.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

Genes affected

ABHD3 (HGNC:18718): (abhydrolase domain containing 3, phospholipase) This gene encodes a protein containing an alpha/beta hydrolase fold, which is a catalytic domain found in a very wide range of enzymes. The function of this protein has not been determined. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABHD3	NM_138340.5	c.555+2468G>A		intron_variant		ENST00000289119.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABHD3	ENST00000289119.7	c.555+2468G>A		intron_variant		1	NM_138340.5	P1
	ENST00000578583.1	n.37-699C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22432 AN: 151936 Hom.: 1985 Cov.: 31

Gnomad AFR AF: 0.0668

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.148 AC: 22431 AN: 152054 Hom.: 1983 Cov.: 31 AF XY: 0.147 AC XY: 10906 AN XY: 74326

Gnomad4 AFR AF: 0.0668

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.0239

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.158

Alfa AF: 0.186 Hom.: 4985

Bravo AF: 0.134

Asia WGS AF: 0.0990 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.9
Dann	Benign	0.59

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

LitVar

Other links and lift over

dbSNP: rs11662721; hg19: chr18-19261413;