Variant 14-104924668-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The 14-104924668-C-T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,168 control chromosomes in the GnomAD database, including 14,087 homozygotes. 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: 𝑓 0.42 ( 14076 hom., cov: 32)

Exomes 𝑓: 0.42 ( 11 hom. )

Consequence

PLD4
ENST00000649344.1 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.97

Variant links:

Genes affected

PLD4 (HGNC:23792): (phospholipase D family member 4) Predicted to enable single-stranded DNA 5'-3' exodeoxyribonuclease activity. Predicted to be involved in hematopoietic progenitor cell differentiation; phagocytosis; and regulation of cytokine production involved in inflammatory response. Predicted to be located in early endosome and endoplasmic reticulum membrane. Predicted to be active in several cellular components, including endoplasmic reticulum; phagocytic vesicle; and trans-Golgi network membrane. [provided by Alliance of Genome Resources, Apr 2022]

PLD4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 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
PLD4	ENST00000649344.1 linkuse as main transcript			upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.416

AC:

63144

AN:

151958

Hom.:

14073

Cov.:

show subpopulations

Gnomad AFR

AF:

0.256

Gnomad AMI

AF:

0.598

Gnomad AMR

AF:

0.449

Gnomad ASJ

AF:

0.349

Gnomad EAS

AF:

0.598

Gnomad SAS

AF:

0.422

Gnomad FIN

AF:

0.590

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.465

Gnomad OTH

AF:

0.419

GnomAD4 exome

AF:

0.424

AC:

AN:

Hom.:

AF XY:

0.392

AC XY:

AN XY:

show subpopulations

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.419

GnomAD4 genome

AF:

0.415

AC:

63166

AN:

152076

Hom.:

14076

Cov.:

AF XY:

0.422

AC XY:

31331

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.256

Gnomad4 AMR

AF:

0.449

Gnomad4 ASJ

AF:

0.349

Gnomad4 EAS

AF:

0.598

Gnomad4 SAS

AF:

0.421

Gnomad4 FIN

AF:

0.590

Gnomad4 NFE

AF:

0.465

Gnomad4 OTH

AF:

0.419

Alfa

AF:

0.442

Hom.:

24281

Bravo

AF:

0.400

Asia WGS

AF:

0.448

AC:

1557

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

Cadd

Benign

0.085

Dann

Benign

0.66

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over