chr20-63861740-T-C

Variant names:

• chr20-63861740-T-C
• rs1277613288
• NM_080622.4:c.200T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_080622.4(ABHD16B):​c.200T>C​(p.Leu67Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000907 in 1,410,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00010 (0 hom.)
• Consequence: ABHD16B NM_080622.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.0500
• Publications: 0 publications found

Genes affected

ABHD16B (HGNC:16128): (abhydrolase domain containing 16B) Predicted to enable acylglycerol lipase activity; palmitoyl-(protein) hydrolase activity; and phospholipase activity. Predicted to be involved in monoacylglycerol catabolic process and phosphatidylserine catabolic process. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000268858 (HGNC:58392):

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=0.21669039).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080622.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABHD16B	NM_080622.4	MANE Select	c.200T>C	p.Leu67Pro	missense	Exon 1 of 1	NP_542189.1	Q9H3Z7
	ABHD16B-AS1	NR_165198.1		n.2683A>G		non_coding_transcript_exon	Exon 2 of 2
	ABHD16B-AS1	NR_165312.1		n.3334A>G		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABHD16B	ENST00000369916.5	TSL:6 MANE Select	c.200T>C	p.Leu67Pro	missense	Exon 1 of 1	ENSP00000358932.3	Q9H3Z7
	ENSG00000268858	ENST00000601296.3	TSL:6	n.3484A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.00000661 AC: 1 AN: 151346 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000148

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000101 AC: 127 AN: 1259402 Hom.: 0 Cov.: 32 AF XY: 0.0000925 AC XY: 57 AN XY: 615898

African (AFR) AF: 0.00 AC: 0 AN: 24044

American (AMR) AF: 0.00 AC: 0 AN: 14354

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18468

East Asian (EAS) AF: 0.00 AC: 0 AN: 28096

South Asian (SAS) AF: 0.00 AC: 0 AN: 62446

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31600

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4046

European-Non Finnish (NFE) AF: 0.000122 AC: 125 AN: 1024682

Other (OTH) AF: 0.0000387 AC: 2 AN: 51666

GnomAD4 genome AF: 0.00000661 AC: 1 AN: 151346 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 73922

African (AFR) AF: 0.00 AC: 0 AN: 41292

American (AMR) AF: 0.00 AC: 0 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5136

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10366

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.0000148 AC: 1 AN: 67786

Other (OTH) AF: 0.00 AC: 0 AN: 2076

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.053
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	13
DANN	Uncertain	0.99
DEOGEN2	Benign	0.00098	T
Eigen	Benign	-0.13
Eigen_PC	Benign	-0.29
FATHMM_MKL	Benign	0.076	N
LIST_S2	Benign	0.38	T
M_CAP	Uncertain	0.099	D
MetaRNN	Benign	0.22	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Uncertain	2.2	M
PhyloP100		-0.050
PrimateAI	Pathogenic	0.83	D
PROVEAN	Benign	-0.34	N
REVEL	Benign	0.15
Sift	Benign	0.22	T
Sift4G	Benign	0.31	T
Polyphen		0.98	D
Vest4		0.20
MutPred		0.34		Loss of stability (P = 0.0098)
MVP		0.42
MPC		1.1
ClinPred		0.34	T
GERP RS		3.1
PromoterAI		-0.12	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.98
Varity_R		0.046
gMVP		0.48
Mutation Taster		=98/2	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: rs1277613288; hg19: chr20-62493093;