rs9587535

Variant names:

• chr13-108230400-A-C
• rs9587535
• NM_032859.3:c.*168A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-108230400-A-C
• chr13-108230400-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_032859.3(ABHD13):​c.*168A>C variant causes a 3 prime UTR change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ABHD13 NM_032859.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.35
• Publications: 9 publications found

Genes affected

ABHD13 (HGNC:20293): (abhydrolase domain containing 13) Predicted to enable palmitoyl-(protein) hydrolase activity. Predicted to be involved in protein depalmitoylation. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABHD13	NM_032859.3	c.*168A>C		3_prime_UTR_variant	Exon 2 of 2	ENST00000375898.4	NP_116248.2
ABHD13	XM_011521128.4	c.*168A>C		3_prime_UTR_variant	Exon 2 of 2		XP_011519430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABHD13	ENST00000375898.4	c.*168A>C		3_prime_UTR_variant	Exon 2 of 2	1	NM_032859.3	ENSP00000365063.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 442200 Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0 AN XY: 228420

African (AFR) AF: 0.00 AC: 0 AN: 11266

American (AMR) AF: 0.00 AC: 0 AN: 12386

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12524

East Asian (EAS) AF: 0.00 AC: 0 AN: 27796

South Asian (SAS) AF: 0.00 AC: 0 AN: 32536

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40364

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1810

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 279242

Other (OTH) AF: 0.00 AC: 0 AN: 24276

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.3
DANN	Benign	0.57
PhyloP100		4.4

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: rs9587535; hg19: chr13-108882748;