Variant 12-109855760-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_016433.4(GLTP):c.306C>A(p.Arg102Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00659 in 1,598,864 control chromosomes in the GnomAD database, including 69 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0056 ( 5 hom., cov: 31)

Exomes 𝑓: 0.0067 ( 64 hom. )

Consequence

GLTP
NM_016433.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.396

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 -21 ACMG points.

BP4

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

BP6

Variant 12-109855760-G-T is Benign according to our data. Variant chr12-109855760-G-T is described in ClinVar as [Benign]. Clinvar id is 774904.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.396 with no splicing effect.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00557 (846/151854) while in subpopulation SAS AF= 0.0196 (94/4790). AF 95% confidence interval is 0.0164. There are 5 homozygotes in gnomad4. There are 406 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

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.306C>A	p.Arg102Arg	synonymous_variant	4/5	ENST00000318348.9	NP_057517.1	Q9NZD2A0A024RBI7
GLTP	XM_047428937.1 linkuse as main transcript	c.183C>A	p.Arg61Arg	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.306C>A	p.Arg102Arg	synonymous_variant	4/5	1	NM_016433.4	ENSP00000315263.3		Q9NZD2

Frequencies

GnomAD3 genomes

AF:

0.00557

AC:

845

AN:

151736

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00138

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00638

Gnomad ASJ

AF:

0.00663

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0192

Gnomad FIN

AF:

0.00491

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00735

Gnomad OTH

AF:

0.00913

GnomAD3 exomes

AF:

0.00792

AC:

1879

AN:

237208

Hom.:

AF XY:

0.00894

AC XY:

1147

AN XY:

128318

show subpopulations

Gnomad AFR exome

AF:

0.00139

Gnomad AMR exome

AF:

0.00750

Gnomad ASJ exome

AF:

0.00598

Gnomad EAS exome

AF:

0.000116

Gnomad SAS exome

AF:

0.0215

Gnomad FIN exome

AF:

0.00505

Gnomad NFE exome

AF:

0.00738

Gnomad OTH exome

AF:

0.00837

GnomAD4 exome

AF:

0.00670

AC:

9692

AN:

1447010

Hom.:

Cov.:

AF XY:

0.00717

AC XY:

5158

AN XY:

719632

show subpopulations

Gnomad4 AFR exome

AF:

0.000700

Gnomad4 AMR exome

AF:

0.00708

Gnomad4 ASJ exome

AF:

0.00765

Gnomad4 EAS exome

AF:

0.000128

Gnomad4 SAS exome

AF:

0.0198

Gnomad4 FIN exome

AF:

0.00593

Gnomad4 NFE exome

AF:

0.00604

Gnomad4 OTH exome

AF:

0.00713

GnomAD4 genome

AF:

0.00557

AC:

846

AN:

151854

Hom.:

Cov.:

AF XY:

0.00547

AC XY:

406

AN XY:

74212

show subpopulations

Gnomad4 AFR

AF:

0.00138

Gnomad4 AMR

AF:

0.00637

Gnomad4 ASJ

AF:

0.00663

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0196

Gnomad4 FIN

AF:

0.00491

Gnomad4 NFE

AF:

0.00735

Gnomad4 OTH

AF:

0.00904

Alfa

AF:

0.00623

Hom.:

Bravo

AF:

0.00519

Asia WGS

AF:

0.00982

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Nov 14, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

DANN

Benign

0.88

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.17

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