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3-142664448-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001145319.2(PLS1):c.70+141G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 509,706 control chromosomes in the GnomAD database, including 3,726 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.095 ( 911 hom., cov: 32)
Exomes 𝑓: 0.11 ( 2815 hom. )

Consequence

PLS1
NM_001145319.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0100
Variant links:
Genes affected
PLS1 (HGNC:9090): (plastin 1) Plastins are a family of actin-binding proteins that are conserved throughout eukaryote evolution and expressed in most tissues of higher eukaryotes. In humans, two ubiquitous plastin isoforms (L and T) have been identified. The protein encoded by this gene is a third distinct plastin isoform, which is specifically expressed at high levels in the small intestine. Alternatively spliced transcript variants varying in the 5' UTR, but encoding the same protein, have been found for this gene. A pseudogene of this gene is found on chromosome 11.[provided by RefSeq, Feb 2010]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 3-142664448-G-T is Benign according to our data. Variant chr3-142664448-G-T is described in ClinVar as [Benign]. Clinvar id is 1221574.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PLS1NM_001145319.2 linkuse as main transcriptc.70+141G>T intron_variant ENST00000457734.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PLS1ENST00000457734.7 linkuse as main transcriptc.70+141G>T intron_variant 2 NM_001145319.2 P1
ENST00000690164.1 linkuse as main transcriptn.119-7242C>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0951
AC:
14450
AN:
151910
Hom.:
913
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0283
Gnomad AMI
AF:
0.103
Gnomad AMR
AF:
0.0671
Gnomad ASJ
AF:
0.123
Gnomad EAS
AF:
0.000964
Gnomad SAS
AF:
0.0966
Gnomad FIN
AF:
0.226
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.128
Gnomad OTH
AF:
0.0849
GnomAD4 exome
AF:
0.114
AC:
40736
AN:
357678
Hom.:
2815
AF XY:
0.113
AC XY:
21461
AN XY:
189928
show subpopulations
Gnomad4 AFR exome
AF:
0.0286
Gnomad4 AMR exome
AF:
0.0523
Gnomad4 ASJ exome
AF:
0.132
Gnomad4 EAS exome
AF:
0.000398
Gnomad4 SAS exome
AF:
0.0963
Gnomad4 FIN exome
AF:
0.197
Gnomad4 NFE exome
AF:
0.126
Gnomad4 OTH exome
AF:
0.0999
GnomAD4 genome
AF:
0.0950
AC:
14446
AN:
152028
Hom.:
911
Cov.:
32
AF XY:
0.0994
AC XY:
7387
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.0283
Gnomad4 AMR
AF:
0.0671
Gnomad4 ASJ
AF:
0.123
Gnomad4 EAS
AF:
0.000966
Gnomad4 SAS
AF:
0.0959
Gnomad4 FIN
AF:
0.226
Gnomad4 NFE
AF:
0.128
Gnomad4 OTH
AF:
0.0849
Alfa
AF:
0.119
Hom.:
243
Bravo
AF:
0.0784
Asia WGS
AF:
0.0610
AC:
212
AN:
3476

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMay 15, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
Cadd
Benign
7.7
Dann
Benign
0.60

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: rs13075015; hg19: chr3-142383290; API