rs1078107

chr15-80717774-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.590+21755T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0185 in 152,272 control chromosomes in the GnomAD database, including 88 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 0.018 (88 hom., cov: 32)
• Consequence: ABHD17C NM_021214.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABHD17C	NM_021214.2	c.590+21755T>C		intron_variant		ENST00000258884.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABHD17C	ENST00000258884.5	c.590+21755T>C		intron_variant		1	NM_021214.2	P1

Frequencies

GnomAD3 genomes AF: 0.0184 AC: 2796 AN: 152154 Hom.: 84 Cov.: 32

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0885

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.0522

Gnomad SAS AF: 0.0220

Gnomad FIN AF: 0.00254

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00426

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0185 AC: 2814 AN: 152272 Hom.: 88 Cov.: 32 AF XY: 0.0203 AC XY: 1508 AN XY: 74456

Gnomad4 AFR AF: 0.0137

Gnomad4 AMR AF: 0.0895

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.0521

Gnomad4 SAS AF: 0.0220

Gnomad4 FIN AF: 0.00254

Gnomad4 NFE AF: 0.00426

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.0111 Hom.: 54

Bravo AF: 0.0235

Asia WGS AF: 0.0500 AC: 172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.11
Dann	Benign	0.63

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: rs1078107; hg19: chr15-81010115;