rs2295663

Positions:

• chr6-31701518-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ABHD16A	NM_021160.3	c.190-178T>C		intron_variant		ENST00000395952.8
ABHD16A	NM_001177515.2	c.158-490T>C		intron_variant
ABHD16A	NR_033488.2	n.405-178T>C		intron_variant, non_coding_transcript_variant
ABHD16A	NR_033489.2	n.176-490T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABHD16A	ENST00000395952.8	c.190-178T>C		intron_variant		1	NM_021160.3	P1

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

Gnomad4 AFR AF: 0.0103

Gnomad4 AMR AF: 0.0325

Gnomad4 ASJ AF: 0.0599

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0330

Gnomad4 NFE AF: 0.0570

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0572 Hom.: 351

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

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

Publications

LitVar

Other links and lift over

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