rs1898153

Variant summary

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

The ENST00000536534.7(PLD5):​c.736-4827G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,014 control chromosomes in the GnomAD database, including 11,994 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 0.38 ( 11994 hom., cov: 33)

Consequence

PLD5
ENST00000536534.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.236
Variant links:
Genes affected
PLD5 (HGNC:26879): (phospholipase D family member 5) Predicted to enable catalytic activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PLD5NM_001372062.1 linkuse as main transcriptc.736-4827G>A intron_variant ENST00000536534.7 NP_001358991.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PLD5ENST00000536534.7 linkuse as main transcriptc.736-4827G>A intron_variant 1 NM_001372062.1 ENSP00000440896 P1Q8N7P1-1

Frequencies

GnomAD3 genomes
AF:
0.385
AC:
58417
AN:
151898
Hom.:
11989
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.258
Gnomad AMI
AF:
0.411
Gnomad AMR
AF:
0.472
Gnomad ASJ
AF:
0.342
Gnomad EAS
AF:
0.610
Gnomad SAS
AF:
0.485
Gnomad FIN
AF:
0.435
Gnomad MID
AF:
0.386
Gnomad NFE
AF:
0.411
Gnomad OTH
AF:
0.397
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.384
AC:
58444
AN:
152014
Hom.:
11994
Cov.:
33
AF XY:
0.388
AC XY:
28804
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.258
Gnomad4 AMR
AF:
0.472
Gnomad4 ASJ
AF:
0.342
Gnomad4 EAS
AF:
0.610
Gnomad4 SAS
AF:
0.485
Gnomad4 FIN
AF:
0.435
Gnomad4 NFE
AF:
0.411
Gnomad4 OTH
AF:
0.398
Alfa
AF:
0.392
Hom.:
2077
Bravo
AF:
0.382
Asia WGS
AF:
0.518
AC:
1802
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
5.6
DANN
Benign
0.79

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.

Other links and lift over

dbSNP: rs1898153; hg19: chr1-242292794; API