rs7171423

chr15-80737287-T-C

Variant summary

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

The NM_021214.2(ABHD17C):c.591-12226T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,186 control chromosomes in the GnomAD database, including 1,938 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 0.15 (1938 hom., cov: 32)
• Consequence: ABHD17C NM_021214.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABHD17C	NM_021214.2	c.591-12226T>C		intron_variant		ENST00000258884.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABHD17C	ENST00000258884.5	c.591-12226T>C		intron_variant		1	NM_021214.2	P1

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23109 AN: 152068 Hom.: 1919 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.152 AC: 23182 AN: 152186 Hom.: 1938 Cov.: 32 AF XY: 0.156 AC XY: 11639 AN XY: 74412

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.155

Alfa AF: 0.161 Hom.: 328

Bravo AF: 0.154

Asia WGS AF: 0.197 AC: 685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.80
Dann	Benign	0.33

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: rs7171423; hg19: chr15-81029628;