13-108230400-A-G

Position:

• chr13-108230400-A-G

Variant summary

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

The NM_032859.3(ABHD13):​c.*168A>G variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.106 in 592,356 control chromosomes in the GnomAD database, including 3,607 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 0.11 (887 hom., cov: 32)
  • Exomes 𝑓: 0.11 (2720 hom.)
• Consequence: ABHD13 NM_032859.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.35

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABHD13	NM_032859.3	c.*168A>G		3_prime_UTR_variant	2/2	ENST00000375898.4	NP_116248.2
ABHD13	XM_011521128.4	c.*168A>G		3_prime_UTR_variant	2/2		XP_011519430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABHD13	ENST00000375898.4	c.*168A>G		3_prime_UTR_variant	2/2	1	NM_032859.3	ENSP00000365063.3

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16079 AN: 150474 Hom.: 886 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0333

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0991

Gnomad FIN AF: 0.0875

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.110

GnomAD4 exome AF: 0.106 AC: 46804 AN: 441768 Hom.: 2720 Cov.: 6 AF XY: 0.106 AC XY: 24120 AN XY: 228212

Gnomad4 AFR exome AF: 0.103

Gnomad4 AMR exome AF: 0.139

Gnomad4 ASJ exome AF: 0.188

Gnomad4 EAS exome AF: 0.102

Gnomad4 SAS exome AF: 0.106

Gnomad4 FIN exome AF: 0.0947

Gnomad4 NFE exome AF: 0.101

Gnomad4 OTH exome AF: 0.121

GnomAD4 genome AF: 0.107 AC: 16087 AN: 150588 Hom.: 887 Cov.: 32 AF XY: 0.105 AC XY: 7763 AN XY: 73614

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.0988

Gnomad4 FIN AF: 0.0875

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.112

Alfa AF: 0.104 Hom.: 383

Bravo AF: 0.112

Asia WGS AF: 0.140 AC: 482 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.6
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: rs9587535; hg19: chr13-108882748; COSMIC: COSV65535454;