rs6848982

chr4-128038058-G-Achr4-128038058-G-T

Variant summary

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

The NM_001358451.3(ABHD18):c.*2245G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,082 control chromosomes in the GnomAD database, including 2,400 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 0.16 (2400 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ABHD18 NM_001358451.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332

Genes affected

ABHD18 (HGNC:26111): (abhydrolase domain containing 18) Predicted to be located in extracellular region. [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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABHD18	NM_001358451.3	c.*2245G>A		3_prime_UTR_variant	13/13	ENST00000645843.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABHD18	ENST00000645843.2	c.*2245G>A		3_prime_UTR_variant	13/13		NM_001358451.3	P1
ABHD18	ENST00000388795.10	c.*3398G>A		3_prime_UTR_variant, NMD_transcript_variant	13/13	5

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23899 AN: 151964 Hom.: 2399 Cov.: 32

Gnomad AFR AF: 0.0399

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.192

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.157 AC: 23911 AN: 152082 Hom.: 2400 Cov.: 32 AF XY: 0.160 AC XY: 11898 AN XY: 74320

Gnomad4 AFR AF: 0.0397

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.195

Alfa AF: 0.111 Hom.: 237

Bravo AF: 0.152

Asia WGS AF: 0.203 AC: 706 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	1.9
Dann	Benign	0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6848982; hg19: chr4-128959213;