rs12148329

chr15-80708937-T-G

Variant summary

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

The NM_021214.2(ABHD17C):c.590+12918T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 151,984 control chromosomes in the GnomAD database, including 1,300 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 0.13 (1300 hom., cov: 32)
• Consequence: ABHD17C NM_021214.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.408

Genes affected

ABHD17C (HGNC:26925): (abhydrolase domain containing 17C, depalmitoylase) Enables palmitoyl-(protein) hydrolase activity. Involved in protein depalmitoylation. Predicted to be located in postsynaptic density. Predicted to be active in endosome membrane; glutamatergic synapse; and plasma 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABHD17C	NM_021214.2	c.590+12918T>G		intron_variant		ENST00000258884.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABHD17C	ENST00000258884.5	c.590+12918T>G		intron_variant		1	NM_021214.2	P1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19328 AN: 151866 Hom.: 1298 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.127 AC: 19339 AN: 151984 Hom.: 1300 Cov.: 32 AF XY: 0.129 AC XY: 9558 AN XY: 74288

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0826

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.129

Alfa AF: 0.138 Hom.: 2535

Bravo AF: 0.120

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	7.3
Dann	Benign	0.71

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: rs12148329; hg19: chr15-81001278;