3-193265909-A-G

Variant summary

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

The NM_020386.5(PLAAT1):​c.405+2674A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,942 control chromosomes in the GnomAD database, including 14,083 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 ( 14083 hom., cov: 32)

Consequence

PLAAT1
NM_020386.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18
Variant links:
Genes affected
PLAAT1 (HGNC:14922): (phospholipase A and acyltransferase 1) Enables acyltransferase activity, transferring groups other than amino-acyl groups and phospholipase activity. Involved in N-acylphosphatidylethanolamine metabolic process and phosphatidylcholine metabolic process. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PLAAT1NM_020386.5 linkc.405+2674A>G intron_variant ENST00000264735.4 NP_065119.3 Q9HDD0-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PLAAT1ENST00000264735.4 linkc.405+2674A>G intron_variant 1 NM_020386.5 ENSP00000264735.4 Q9HDD0-1
PLAAT1ENST00000650797.1 linkc.720+2674A>G intron_variant ENSP00000498228.1 Q9HDD0-2
PLAAT1ENST00000416012.1 linkn.234+2674A>G intron_variant 5 ENSP00000414431.1 H7C3Y1

Frequencies

GnomAD3 genomes
AF:
0.416
AC:
63171
AN:
151824
Hom.:
14080
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.562
Gnomad AMI
AF:
0.292
Gnomad AMR
AF:
0.370
Gnomad ASJ
AF:
0.400
Gnomad EAS
AF:
0.549
Gnomad SAS
AF:
0.493
Gnomad FIN
AF:
0.285
Gnomad MID
AF:
0.389
Gnomad NFE
AF:
0.344
Gnomad OTH
AF:
0.434
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.416
AC:
63219
AN:
151942
Hom.:
14083
Cov.:
32
AF XY:
0.414
AC XY:
30743
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.562
Gnomad4 AMR
AF:
0.370
Gnomad4 ASJ
AF:
0.400
Gnomad4 EAS
AF:
0.548
Gnomad4 SAS
AF:
0.492
Gnomad4 FIN
AF:
0.285
Gnomad4 NFE
AF:
0.344
Gnomad4 OTH
AF:
0.437
Alfa
AF:
0.375
Hom.:
5584
Bravo
AF:
0.431
Asia WGS
AF:
0.537
AC:
1865
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
5.2
DANN
Benign
0.70

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: rs3905277; hg19: chr3-192983698; API