6-31688237-C-CCACG

Position:

• chr6-31688237-C-CCACG

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_021160.3(ABHD16A):​c.1307+11_1307+12insCGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00621 in 1,613,848 control chromosomes in the GnomAD database, including 54 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0058 (8 hom., cov: 32)
  • Exomes 𝑓: 0.0062 (46 hom.)
• Consequence: ABHD16A NM_021160.3 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.952

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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 6-31688237-C-CCACG is Benign according to our data. Variant chr6-31688237-C-CCACG is described in ClinVar as [Likely_benign]. Clinvar id is 2571245.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABHD16A	NM_021160.3	c.1307+11_1307+12insCGTG		intron_variant		ENST00000395952.8	NP_066983.1
ABHD16A	NM_001177515.2	c.1208+11_1208+12insCGTG		intron_variant			NP_001170986.1
ABHD16A	NR_033488.2	n.1522+11_1522+12insCGTG		intron_variant, non_coding_transcript_variant
ABHD16A	NR_033489.2	n.1226+11_1226+12insCGTG		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABHD16A	ENST00000395952.8	c.1307+11_1307+12insCGTG		intron_variant		1	NM_021160.3	ENSP00000379282	P1

Frequencies

GnomAD3 genomes AF: 0.00583 AC: 887 AN: 152090 Hom.: 8 Cov.: 32

Gnomad AFR AF: 0.00109

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.00694

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00774

Gnomad OTH AF: 0.00526

GnomAD3 exomes AF: 0.00517 AC: 1300 AN: 251254 Hom.: 8 AF XY: 0.00535 AC XY: 727 AN XY: 135786

Gnomad AFR exome AF: 0.00111

Gnomad AMR exome AF: 0.00350

Gnomad ASJ exome AF: 0.00478

Gnomad EAS exome AF: 0.000272

Gnomad SAS exome AF: 0.00252

Gnomad FIN exome AF: 0.0108

Gnomad NFE exome AF: 0.00670

Gnomad OTH exome AF: 0.00604

GnomAD4 exome AF: 0.00625 AC: 9130 AN: 1461640 Hom.: 46 Cov.: 32 AF XY: 0.00632 AC XY: 4592 AN XY: 727150

Gnomad4 AFR exome AF: 0.000986

Gnomad4 AMR exome AF: 0.00407

Gnomad4 ASJ exome AF: 0.00490

Gnomad4 EAS exome AF: 0.000151

Gnomad4 SAS exome AF: 0.00247

Gnomad4 FIN exome AF: 0.0105

Gnomad4 NFE exome AF: 0.00690

Gnomad4 OTH exome AF: 0.00515

GnomAD4 genome AF: 0.00583 AC: 888 AN: 152208 Hom.: 8 Cov.: 32 AF XY: 0.00586 AC XY: 436 AN XY: 74404

Gnomad4 AFR AF: 0.00108

Gnomad4 AMR AF: 0.00693

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00187

Gnomad4 FIN AF: 0.0113

Gnomad4 NFE AF: 0.00774

Gnomad4 OTH AF: 0.00521

Alfa AF: 0.00727 Hom.: 1

Bravo AF: 0.00544

Asia WGS AF: 0.00491 AC: 17 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2024

ABHD16A: BS2 -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9281554; hg19: chr6-31656014;