rs1473792

Variant names:

• chr13-108225281-T-C
• rs1473792
• NM_032859.3:c.-20-3918T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ABHD13	NM_032859.3	c.-20-3918T>C		intron_variant	Intron 1 of 1	ENST00000375898.4	NP_116248.2
ABHD13	XM_011521128.4	c.-20-3918T>C		intron_variant	Intron 1 of 1		XP_011519430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABHD13	ENST00000375898.4	c.-20-3918T>C		intron_variant	Intron 1 of 1	1	NM_032859.3	ENSP00000365063.3

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

African (AFR) AF: 0.0735 AC: 3050 AN: 41502

American (AMR) AF: 0.117 AC: 1780 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 691 AN: 3470

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5170

South Asian (SAS) AF: 0.0598 AC: 288 AN: 4816

European-Finnish (FIN) AF: 0.216 AC: 2285 AN: 10556

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12670 AN: 67982

Other (OTH) AF: 0.160 AC: 338 AN: 2110

Alfa AF: 0.171 Hom.: 1230

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
PhyloP100		-0.87
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: rs1473792; hg19: chr13-108877629;