Variant 6-31688737-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_021160.3(ABHD16A):c.1236G>A(p.Ala412Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 1,612,990 control chromosomes in the GnomAD database, including 135 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0073 ( 10 hom., cov: 32)

Exomes 𝑓: 0.011 ( 125 hom. )

Consequence

ABHD16A
NM_021160.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.56

Variant links:

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 links:

ENSG00000204422 (HGNC:):

ENSG00000204422 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 6-31688737-C-T is Benign according to our data. Variant chr6-31688737-C-T is described in ClinVar as [Benign]. Clinvar id is 2571246.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-3.56 with no splicing effect.

BS1

Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.0111 (16264/1460670) while in subpopulation EAS AF= 0.0381 (1512/39698). AF 95% confidence interval is 0.0365. There are 125 homozygotes in gnomad4_exome. There are 8010 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABHD16A	NM_021160.3 linkuse as main transcript	c.1236G>A	p.Ala412Ala	synonymous_variant	14/20	ENST00000395952.8	NP_066983.1	O95870-1A0A1U9X777
ABHD16A	NM_001177515.2 linkuse as main transcript	c.1137G>A	p.Ala379Ala	synonymous_variant	12/18		NP_001170986.1	O95870-2B3KNX9
ABHD16A	NR_033488.2 linkuse as main transcript	n.1451G>A		non_coding_transcript_exon_variant	14/20
ABHD16A	NR_033489.2 linkuse as main transcript	n.1155G>A		non_coding_transcript_exon_variant	12/18

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABHD16A	ENST00000395952.8 linkuse as main transcript	c.1236G>A	p.Ala412Ala	synonymous_variant	14/20	1	NM_021160.3	ENSP00000379282.3		O95870-1

Frequencies

GnomAD3 genomes

AF:

0.00730

AC:

1111

AN:

152202

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00162

Gnomad AMI

AF:

0.0504

Gnomad AMR

AF:

0.00922

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.0100

Gnomad SAS

AF:

0.00331

Gnomad FIN

AF:

0.00470

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0105

Gnomad OTH

AF:

0.00669

GnomAD3 exomes

AF:

0.00798

AC:

1966

AN:

246288

Hom.:

AF XY:

0.00794

AC XY:

1066

AN XY:

134274

show subpopulations

Gnomad AFR exome

AF:

0.00133

Gnomad AMR exome

AF:

0.00717

Gnomad ASJ exome

AF:

0.00251

Gnomad EAS exome

AF:

0.0136

Gnomad SAS exome

AF:

0.00250

Gnomad FIN exome

AF:

0.00551

Gnomad NFE exome

AF:

0.0108

Gnomad OTH exome

AF:

0.00643

GnomAD4 exome

AF:

0.0111

AC:

16264

AN:

1460670

Hom.:

125

Cov.:

AF XY:

0.0110

AC XY:

8010

AN XY:

726654

show subpopulations

Gnomad4 AFR exome

AF:

0.00119

Gnomad4 AMR exome

AF:

0.00700

Gnomad4 ASJ exome

AF:

0.00356

Gnomad4 EAS exome

AF:

0.0381

Gnomad4 SAS exome

AF:

0.00286

Gnomad4 FIN exome

AF:

0.00618

Gnomad4 NFE exome

AF:

0.0119

Gnomad4 OTH exome

AF:

0.00755

GnomAD4 genome

AF:

0.00730

AC:

1112

AN:

152320

Hom.:

Cov.:

AF XY:

0.00690

AC XY:

514

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.00161

Gnomad4 AMR

AF:

0.00921

Gnomad4 ASJ

AF:

0.00346

Gnomad4 EAS

AF:

0.0100

Gnomad4 SAS

AF:

0.00331

Gnomad4 FIN

AF:

0.00470

Gnomad4 NFE

AF:

0.0105

Gnomad4 OTH

AF:

0.00662

Alfa

AF:

0.00852

Hom.:

Bravo

AF:

0.00701

Asia WGS

AF:

0.00866

AC:

AN:

3478

EpiCase

AF:

0.00851

EpiControl

AF:

0.00996

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2024

ABHD16A: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

6.2

DANN

Benign

0.88

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over