rs1473792

chr13-108225281-T-C

Variant summary

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

The NM_032859.3(ABHD13):c.-20-3918T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,074 control chromosomes in the GnomAD database, including 1,814 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 0.14 (1814 hom., cov: 32)
• Consequence: ABHD13 NM_032859.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870

Genes affected

ABHD13 (HGNC:20293): (abhydrolase domain containing 13) Predicted to enable palmitoyl-(protein) hydrolase activity. Predicted to be involved in protein depalmitoylation. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABHD13	NM_032859.3	c.-20-3918T>C		intron_variant		ENST00000375898.4
ABHD13	XM_011521128.4	c.-20-3918T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABHD13	ENST00000375898.4	c.-20-3918T>C		intron_variant		1	NM_032859.3	P1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21338 AN: 151958 Hom.: 1814 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0587

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.140 AC: 21339 AN: 152074 Hom.: 1814 Cov.: 32 AF XY: 0.139 AC XY: 10366 AN XY: 74336

Gnomad4 AFR AF: 0.0735

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.0598

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.160

Alfa AF: 0.171 Hom.: 1102

Bravo AF: 0.130

Asia WGS AF: 0.0340 AC: 117 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	6.7
Dann	Benign	0.60

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: rs1473792; hg19: chr13-108877629;