6-31701719-C-T

Variant names:

• chr6-31701719-C-T
• rs1266071
• NM_021160.3:c.189+355G>A

Variant summary

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

The NM_021160.3(ABHD16A):​c.189+355G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0667 in 152,254 control chromosomes in the GnomAD database, including 472 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 0.067 (472 hom., cov: 32)
• Consequence: ABHD16A NM_021160.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07
• Publications: 24 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=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.096 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABHD16A	NM_021160.3	c.189+355G>A		intron_variant	Intron 2 of 19	ENST00000395952.8	NP_066983.1
ABHD16A	NM_001177515.2	c.158-691G>A		intron_variant	Intron 1 of 17		NP_001170986.1
ABHD16A	NR_033488.2	n.404+355G>A		intron_variant	Intron 2 of 19
ABHD16A	NR_033489.2	n.176-691G>A		intron_variant	Intron 1 of 17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABHD16A	ENST00000395952.8	c.189+355G>A		intron_variant	Intron 2 of 19	1	NM_021160.3	ENSP00000379282.3

Frequencies

GnomAD3 genomes AF: 0.0668 AC: 10166 AN: 152136 Hom.: 471 Cov.: 32

Gnomad AFR AF: 0.0182

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.0673

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0980

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.0667 AC: 10162 AN: 152254 Hom.: 472 Cov.: 32 AF XY: 0.0651 AC XY: 4844 AN XY: 74434

African (AFR) AF: 0.0181 AC: 753 AN: 41546

American (AMR) AF: 0.0630 AC: 964 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 491 AN: 3472

East Asian (EAS) AF: 0.0181 AC: 94 AN: 5184

South Asian (SAS) AF: 0.0366 AC: 177 AN: 4832

European-Finnish (FIN) AF: 0.0673 AC: 713 AN: 10596

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0980 AC: 6662 AN: 68010

Other (OTH) AF: 0.0720 AC: 152 AN: 2112

Alfa AF: 0.0834 Hom.: 1645

Bravo AF: 0.0647

Asia WGS AF: 0.0290 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	19
DANN	Benign	0.58
PhyloP100		2.1
Mutation Taster		=99/1	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: rs1266071; hg19: chr6-31669496;