4-128038058-G-T

Variant names:

• chr4-128038058-G-T
• rs6848982
• ENST00000388795.10:n.*3398G>T

Variant summary

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

The ENST00000388795.10(ABHD18):​n.*3398G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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)
• Consequence: ABHD18 ENST00000388795.10 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 2 publications found

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

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=-0.79).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000388795.10. 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
	ABHD18	NM_001358451.3	MANE Select	c.*2245G>T		3_prime_UTR	Exon 13 of 13	NP_001345380.1
	ABHD18	NM_001358454.3		c.*2245G>T		3_prime_UTR	Exon 14 of 14	NP_001345383.1
	ABHD18	NM_001366039.3		c.*2245G>T		3_prime_UTR	Exon 12 of 12	NP_001352968.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABHD18	ENST00000388795.10	TSL:5	n.*3398G>T		non_coding_transcript_exon	Exon 13 of 13	ENSP00000373447.6
	ABHD18	ENST00000645843.2	MANE Select	c.*2245G>T		3_prime_UTR	Exon 13 of 13	ENSP00000496010.1
	ABHD18	ENST00000388795.10	TSL:5	n.*3398G>T		3_prime_UTR	Exon 13 of 13	ENSP00000373447.6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 3835

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.6
DANN	Benign	0.58
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs6848982; hg19: chr4-128959213;