rs6848982

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-128038058-G-A
• chr4-128038058-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000388795.10(ABHD18):​n.*3398G>A variant causes a non coding transcript exon 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 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: Benign. The variant received -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.

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>A		3_prime_UTR	Exon 13 of 13	NP_001345380.1
	ABHD18	NM_001358454.3		c.*2245G>A		3_prime_UTR	Exon 14 of 14	NP_001345383.1
	ABHD18	NM_001366039.3		c.*2245G>A		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>A		non_coding_transcript_exon	Exon 13 of 13	ENSP00000373447.6
	ABHD18	ENST00000645843.2	MANE Select	c.*2245G>A		3_prime_UTR	Exon 13 of 13	ENSP00000496010.1
	ABHD18	ENST00000388795.10	TSL:5	n.*3398G>A		3_prime_UTR	Exon 13 of 13	ENSP00000373447.6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0397 AC: 1649 AN: 41516

American (AMR) AF: 0.211 AC: 3220 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 916 AN: 3468

East Asian (EAS) AF: 0.139 AC: 718 AN: 5156

South Asian (SAS) AF: 0.279 AC: 1347 AN: 4828

European-Finnish (FIN) AF: 0.183 AC: 1932 AN: 10564

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13529 AN: 67982

Other (OTH) AF: 0.195 AC: 411 AN: 2106

Alfa AF: 0.173 Hom.: 3835

Bravo AF: 0.152

Asia WGS AF: 0.203 AC: 706 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

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;