3-142678237-CT-C

Variant summary

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

The NM_001145319.2(PLS1):c.579+134del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0142 in 349,494 control chromosomes in the GnomAD database, including 86 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.019 (79 hom., cov: 31)
  • Exomes 𝑓: 0.011 (7 hom.)
• Consequence: PLS1 NM_001145319.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.254

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-142678237-CT-C is Benign according to our data. Variant chr3-142678237-CT-C is described in ClinVar as [Benign]. Clinvar id is 1245176.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLS1	NM_001145319.2	c.579+134del		intron_variant		ENST00000457734.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLS1	ENST00000457734.7	c.579+134del		intron_variant		2	NM_001145319.2	P1
	ENST00000690164.1	n.119-21032del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0190 AC: 2792 AN: 147318 Hom.: 77 Cov.: 31

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00821

Gnomad ASJ AF: 0.000294

Gnomad EAS AF: 0.00334

Gnomad SAS AF: 0.00216

Gnomad FIN AF: 0.000627

Gnomad MID AF: 0.00325

Gnomad NFE AF: 0.000527

Gnomad OTH AF: 0.0155

GnomAD4 exome AF: 0.0106 AC: 2149 AN: 202082 Hom.: 7 AF XY: 0.0103 AC XY: 1083 AN XY: 104844

Gnomad4 AFR exome AF: 0.0596

Gnomad4 AMR exome AF: 0.0154

Gnomad4 ASJ exome AF: 0.00950

Gnomad4 EAS exome AF: 0.0105

Gnomad4 SAS exome AF: 0.0109

Gnomad4 FIN exome AF: 0.00674

Gnomad4 NFE exome AF: 0.00880

Gnomad4 OTH exome AF: 0.0168

GnomAD4 genome AF: 0.0190 AC: 2806 AN: 147412 Hom.: 79 Cov.: 31 AF XY: 0.0187 AC XY: 1341 AN XY: 71778

Gnomad4 AFR AF: 0.0639

Gnomad4 AMR AF: 0.00820

Gnomad4 ASJ AF: 0.000294

Gnomad4 EAS AF: 0.00335

Gnomad4 SAS AF: 0.00217

Gnomad4 FIN AF: 0.000627

Gnomad4 NFE AF: 0.000527

Gnomad4 OTH AF: 0.0154

Bravo AF: 0.0203

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

May 22, 2021

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Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs376338369; hg19: chr3-142397079;