NM_032859.3:c.-21+908G>C

Variant names:

• chr13-108219567-G-C
• rs12428162
• NM_032859.3:c.-21+908G>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.-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
• Publications: 3 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=-0.92).
• 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 rank	MANE	Protein	UniProt
ABHD13	NM_032859.3	c.-21+908G>C		intron_variant	Intron 1 of 1	ENST00000375898.4	NP_116248.2
ABHD13	XM_011521128.4	c.-21+620G>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.-21+908G>C		intron_variant	Intron 1 of 1	1	NM_032859.3	ENSP00000365063.3

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

African (AFR) AF: 0.176 AC: 7293 AN: 41454

American (AMR) AF: 0.288 AC: 4393 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 775 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1021 AN: 5164

South Asian (SAS) AF: 0.113 AC: 546 AN: 4818

European-Finnish (FIN) AF: 0.275 AC: 2901 AN: 10540

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16795 AN: 67976

Other (OTH) AF: 0.236 AC: 498 AN: 2110

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
PhyloP100		-3.1
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: rs12428162; hg19: chr13-108871915;