3-32106485-T-A

Variant names:

• chr3-32106485-T-A
• rs6805518
• ENST00000429432.5:c.-71+656T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000429432.5(GPD1L):​c.-71+656T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 35)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GPD1L ENST00000429432.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 4 publications found

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 Gene-Disease associations (from GenCC):

• Brugada syndrome 2

  Inheritance: AD, Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• Brugada syndrome 1

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429432.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPD1L	NM_015141.4	MANE Select	c.-227T>A		upstream_gene	N/A	NP_055956.1	Q8N335

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPD1L	ENST00000429432.5	TSL:4	c.-71+656T>A		intron	N/A	ENSP00000393861.1	C9K0P5
	GPD1L	ENST00000282541.10	TSL:1 MANE Select	c.-227T>A		upstream_gene	N/A	ENSP00000282541.6	Q8N335
	GPD1L	ENST00000902849.1		c.-227T>A		upstream_gene	N/A	ENSP00000572908.1

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 217284 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 111116

African (AFR) AF: 0.00 AC: 0 AN: 5734

American (AMR) AF: 0.00 AC: 0 AN: 6062

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7520

East Asian (EAS) AF: 0.00 AC: 0 AN: 19378

South Asian (SAS) AF: 0.00 AC: 0 AN: 2244

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 19270

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1098

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 142234

Other (OTH) AF: 0.00 AC: 0 AN: 13744

GnomAD4 genome Cov.: 35

Alfa AF: 0.00 Hom.: 2903

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.20
DANN	Benign	0.75
PhyloP100		-2.4
PromoterAI		-0.12	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6805518; hg19: chr3-32147977;