Variant chr3-32106593-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000429432.5(GPD1L):c.-71+764C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 1,000,430 control chromosomes in the GnomAD database, including 798 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.046 ( 199 hom., cov: 33)

Exomes 𝑓: 0.035 ( 599 hom. )

Consequence

GPD1L
ENST00000429432.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.152

Variant links:

Genes affected

GPD1L (HGNC:28956): (glycerol-3-phosphate dehydrogenase 1 like) The protein encoded by this gene catalyzes the conversion of sn-glycerol 3-phosphate to glycerone phosphate. The encoded protein is found in the cytoplasm, associated with the plasma membrane, where it binds the sodium channel, voltage-gated, type V, alpha subunit (SCN5A). Defects in this gene are a cause of Brugada syndrome type 2 (BRS2) as well as sudden infant death syndrome (SIDS). [provided by RefSeq, Jul 2010]

GPD1L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 3-32106593-C-T is Benign according to our data. Variant chr3-32106593-C-T is described in ClinVar as [Benign]. Clinvar id is 1259211.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPD1L	NM_015141.4 linkuse as main transcript			upstream_gene_variant		ENST00000282541.10	NP_055956.1
GPD1L	XM_006713068.3 linkuse as main transcript			upstream_gene_variant			XP_006713131.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
GPD1L	ENST00000429432.5 linkuse as main transcript	c.-71+764C>T	intron_variant	4		ENSP00000393861
GPD1L	ENST00000282541.10 linkuse as main transcript		upstream_gene_variant	1	NM_015141.4	ENSP00000282541	P1
GPD1L	ENST00000425459.5 linkuse as main transcript		upstream_gene_variant	4		ENSP00000408770
GPD1L	ENST00000428684.1 linkuse as main transcript		upstream_gene_variant	5		ENSP00000392199

Frequencies

GnomAD3 genomes

AF:

0.0464

AC:

7058

AN:

151952

Hom.:

199

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0560

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.0836

Gnomad ASJ

AF:

0.0507

Gnomad EAS

AF:

0.0221

Gnomad SAS

AF:

0.0447

Gnomad FIN

AF:

0.0421

Gnomad MID

AF:

0.102

Gnomad NFE

AF:

0.0337

Gnomad OTH

AF:

0.0459

GnomAD4 exome

AF:

0.0348

AC:

29519

AN:

848370

Hom.:

599

Cov.:

AF XY:

0.0353

AC XY:

14719

AN XY:

417370

show subpopulations

Gnomad4 AFR exome

AF:

0.0620

Gnomad4 AMR exome

AF:

0.101

Gnomad4 ASJ exome

AF:

0.0466

Gnomad4 EAS exome

AF:

0.0265

Gnomad4 SAS exome

AF:

0.0514

Gnomad4 FIN exome

AF:

0.0373

Gnomad4 NFE exome

AF:

0.0317

Gnomad4 OTH exome

AF:

0.0459

GnomAD4 genome

AF:

0.0465

AC:

7066

AN:

152060

Hom.:

199

Cov.:

AF XY:

0.0477

AC XY:

3549

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.0560

Gnomad4 AMR

AF:

0.0835

Gnomad4 ASJ

AF:

0.0507

Gnomad4 EAS

AF:

0.0221

Gnomad4 SAS

AF:

0.0445

Gnomad4 FIN

AF:

0.0421

Gnomad4 NFE

AF:

0.0337

Gnomad4 OTH

AF:

0.0473

Alfa

AF:

0.0430

Hom.:

Bravo

AF:

0.0502

Asia WGS

AF:

0.0540

AC:

185

AN:

3456

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	GeneDx	Mar 03, 2015	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Benign

0.93

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