Variant 12-109855685-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_016433.4(GLTP):c.381C>T(p.Asn127Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0023 in 1,608,010 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0036 ( 5 hom., cov: 30)

Exomes 𝑓: 0.0022 ( 24 hom. )

Consequence

GLTP
NM_016433.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.726

Variant links:

Genes affected

GLTP (HGNC:24867): (glycolipid transfer protein) The protein encoded by this gene is similar to bovine and porcine proteins which accelerate transfer of certain glycosphingolipids and glyceroglycolipids between membranes. It is thought to be a cytoplasmic protein. [provided by RefSeq, Jul 2008]

GLTP 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=-0.41).

BP6

Variant 12-109855685-G-A is Benign according to our data. Variant chr12-109855685-G-A is described in ClinVar as [Benign]. Clinvar id is 774903.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.726 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLTP	NM_016433.4 linkuse as main transcript	c.381C>T	p.Asn127Asn	synonymous_variant	4/5	ENST00000318348.9	NP_057517.1	Q9NZD2A0A024RBI7
GLTP	XM_047428937.1 linkuse as main transcript	c.258C>T	p.Asn86Asn	synonymous_variant	3/4		XP_047284893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLTP	ENST00000318348.9 linkuse as main transcript	c.381C>T	p.Asn127Asn	synonymous_variant	4/5	1	NM_016433.4	ENSP00000315263.3		Q9NZD2

Frequencies

GnomAD3 genomes

AF:

0.00365

AC:

550

AN:

150704

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00616

Gnomad AMI

AF:

0.0199

Gnomad AMR

AF:

0.00254

Gnomad ASJ

AF:

0.0341

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00743

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00118

Gnomad OTH

AF:

0.00389

GnomAD3 exomes

AF:

0.00367

AC:

911

AN:

247946

Hom.:

AF XY:

0.00361

AC XY:

485

AN XY:

134210

show subpopulations

Gnomad AFR exome

AF:

0.00585

Gnomad AMR exome

AF:

0.00370

Gnomad ASJ exome

AF:

0.0308

Gnomad EAS exome

AF:

0.0000561

Gnomad SAS exome

AF:

0.00541

Gnomad FIN exome

AF:

0.000139

Gnomad NFE exome

AF:

0.00161

Gnomad OTH exome

AF:

0.00617

GnomAD4 exome

AF:

0.00216

AC:

3143

AN:

1457188

Hom.:

Cov.:

AF XY:

0.00230

AC XY:

1671

AN XY:

725074

show subpopulations

Gnomad4 AFR exome

AF:

0.00677

Gnomad4 AMR exome

AF:

0.00379

Gnomad4 ASJ exome

AF:

0.0294

Gnomad4 EAS exome

AF:

0.0000763

Gnomad4 SAS exome

AF:

0.00569

Gnomad4 FIN exome

AF:

0.000187

Gnomad4 NFE exome

AF:

0.00106

Gnomad4 OTH exome

AF:

0.00426

GnomAD4 genome

AF:

0.00365

AC:

550

AN:

150822

Hom.:

Cov.:

AF XY:

0.00348

AC XY:

256

AN XY:

73590

show subpopulations

Gnomad4 AFR

AF:

0.00614

Gnomad4 AMR

AF:

0.00253

Gnomad4 ASJ

AF:

0.0341

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00744

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00118

Gnomad4 OTH

AF:

0.00385

Alfa

AF:

0.00462

Hom.:

Bravo

AF:

0.00386

Asia WGS

AF:

0.00231

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	May 11, 2017	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

1.4

DANN

Benign

0.91

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

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