rs12148329

Variant names:

• chr15-80708937-T-G
• rs12148329
• NM_021214.2:c.590+12918T>G

Variant summary

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

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ABHD17C	NM_021214.2	c.590+12918T>G		intron_variant	Intron 1 of 2	ENST00000258884.5	NP_067037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABHD17C	ENST00000258884.5	c.590+12918T>G		intron_variant	Intron 1 of 2	1	NM_021214.2	ENSP00000258884.4

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

African (AFR) AF: 0.108 AC: 4463 AN: 41458

American (AMR) AF: 0.0826 AC: 1261 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3472

East Asian (EAS) AF: 0.170 AC: 873 AN: 5144

South Asian (SAS) AF: 0.105 AC: 504 AN: 4804

European-Finnish (FIN) AF: 0.182 AC: 1926 AN: 10556

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9328 AN: 67972

Other (OTH) AF: 0.129 AC: 273 AN: 2116

Alfa AF: 0.137 Hom.: 6019

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
PhyloP100		0.41
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: rs12148329; hg19: chr15-81001278;