chr15-80717774-T-C

Variant names:

• chr15-80717774-T-C
• rs1078107
• NM_021214.2:c.590+21755T>C

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+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
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0856 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021214.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABHD17C	NM_021214.2	MANE Select	c.590+21755T>C		intron	N/A	NP_067037.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABHD17C	ENST00000258884.5	TSL:1 MANE Select	c.590+21755T>C		intron	N/A	ENSP00000258884.4
	ABHD17C	ENST00000558464.1	TSL:1	c.590+21755T>C		intron	N/A	ENSP00000452778.1
	ABHD17C	ENST00000560609.1	TSL:4	c.-115-31739T>C		intron	N/A	ENSP00000453923.1

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

African (AFR) AF: 0.0137 AC: 571 AN: 41572

American (AMR) AF: 0.0895 AC: 1368 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3472

East Asian (EAS) AF: 0.0521 AC: 270 AN: 5178

South Asian (SAS) AF: 0.0220 AC: 106 AN: 4810

European-Finnish (FIN) AF: 0.00254 AC: 27 AN: 10616

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00426 AC: 290 AN: 68024

Other (OTH) AF: 0.0237 AC: 50 AN: 2112

Alfa AF: 0.0125 Hom.: 70

Bravo AF: 0.0235

Asia WGS AF: 0.0500 AC: 172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.63
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism

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: rs1078107; hg19: chr15-81010115;