rs12428162

Positions:

• chr13-108219567-G-C

Variant summary

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

The NM_032859.3(ABHD13):​c.-21+908G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,000 control chromosomes in the GnomAD database, including 4,123 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 0.23 (4123 hom., cov: 32)
• Consequence: ABHD13 NM_032859.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABHD13	NM_032859.3	c.-21+908G>C		intron_variant		ENST00000375898.4	NP_116248.2
ABHD13	XM_011521128.4	c.-21+620G>C		intron_variant			XP_011519430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABHD13	ENST00000375898.4	c.-21+908G>C		intron_variant		1	NM_032859.3	ENSP00000365063	P1

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34549 AN: 151882 Hom.: 4120 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.228 AC: 34600 AN: 152000 Hom.: 4123 Cov.: 32 AF XY: 0.228 AC XY: 16924 AN XY: 74274

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.236

Alfa AF: 0.243 Hom.: 600

Bravo AF: 0.230

Asia WGS AF: 0.155 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.47
DANN	Benign	0.25

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: rs12428162; hg19: chr13-108871915;