3-32106479-CGGGCCTGGAGGCCGGCCG-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000429432.5(GPD1L):c.-71+656_-71+673del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0129 in 362,064 control chromosomes in the GnomAD database, including 204 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.025 (175 hom., cov: 32)
  • Exomes 𝑓: 0.0040 (29 hom.)
• Consequence: GPD1L ENST00000429432.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.284

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-32106479-CGGGCCTGGAGGCCGGCCG-C is Benign according to our data. Variant chr3-32106479-CGGGCCTGGAGGCCGGCCG-C is described in ClinVar as [Benign]. Clinvar id is 1229730.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPD1L	ENST00000429432.5	c.-71+656_-71+673del		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0252 AC: 3834 AN: 152078 Hom.: 174 Cov.: 32

Gnomad AFR AF: 0.0870

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00903

Gnomad ASJ AF: 0.000577

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.000603

Gnomad OTH AF: 0.0211

GnomAD4 exome AF: 0.00404 AC: 848 AN: 209878 Hom.: 29 AF XY: 0.00354 AC XY: 381 AN XY: 107542

Gnomad4 AFR exome AF: 0.0947

Gnomad4 AMR exome AF: 0.00924

Gnomad4 ASJ exome AF: 0.000409

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000676

Gnomad4 OTH exome AF: 0.0103

GnomAD4 genome AF: 0.0252 AC: 3839 AN: 152186 Hom.: 175 Cov.: 32 AF XY: 0.0241 AC XY: 1793 AN XY: 74408

Gnomad4 AFR AF: 0.0869

Gnomad4 AMR AF: 0.00901

Gnomad4 ASJ AF: 0.000577

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000603

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.0232 Hom.: 6

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 21, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs199516859; hg19: chr3-32147971;