NM_021160.3:c.190-178T>C

Variant names:

• chr6-31701518-A-G
• rs2295663
• NM_021160.3:c.190-178T>C

Variant summary

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

The NM_021160.3(ABHD16A):​c.190-178T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.048 in 152,292 control chromosomes in the GnomAD database, including 325 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 0.048 (325 hom., cov: 32)
• Consequence: ABHD16A NM_021160.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.628
• Publications: 21 publications found

Genes affected

ABHD16A (HGNC:13921): (abhydrolase domain containing 16A, phospholipase) A cluster of genes, BAT1-BAT5, has been localized in the vicinity of the genes for tumor necrosis factor alpha and tumor necrosis factor beta. These genes are all within the human major histocompatibility complex class III region. The protein encoded by this gene is thought to be involved in some aspects of immunity. Alternatively spliced transcript variants have been described. [provided by RefSeq, Apr 2010]

ABHD16A Gene-Disease associations (from GenCC):

• spastic paraplegia 86, autosomal recessive

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)

ENSG00000204422 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABHD16A	NM_021160.3	c.190-178T>C		intron_variant	Intron 2 of 19	ENST00000395952.8	NP_066983.1
ABHD16A	NM_001177515.2	c.158-490T>C		intron_variant	Intron 1 of 17		NP_001170986.1
ABHD16A	NR_033488.2	n.405-178T>C		intron_variant	Intron 2 of 19
ABHD16A	NR_033489.2	n.176-490T>C		intron_variant	Intron 1 of 17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABHD16A	ENST00000395952.8	c.190-178T>C		intron_variant	Intron 2 of 19	1	NM_021160.3	ENSP00000379282.3

Frequencies

GnomAD3 genomes AF: 0.0480 AC: 7307 AN: 152174 Hom.: 325 Cov.: 32

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0324

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0330

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0570

Gnomad OTH AF: 0.0445

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0480 AC: 7305 AN: 152292 Hom.: 325 Cov.: 32 AF XY: 0.0493 AC XY: 3673 AN XY: 74472

African (AFR) AF: 0.0103 AC: 429 AN: 41574

American (AMR) AF: 0.0325 AC: 497 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0599 AC: 208 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1093 AN: 5166

South Asian (SAS) AF: 0.123 AC: 595 AN: 4826

European-Finnish (FIN) AF: 0.0330 AC: 350 AN: 10614

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0570 AC: 3874 AN: 68018

Other (OTH) AF: 0.0464 AC: 98 AN: 2114

Alfa AF: 0.0523 Hom.: 643

Bravo AF: 0.0449

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	11
DANN	Benign	0.69
PhyloP100		0.63
Mutation Taster		=100/0	polymorphism (auto)

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: rs2295663; hg19: chr6-31669295; COSMIC: COSV65451990; COSMIC: COSV65451990;