rs9567638

Variant summary

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

The NM_002298.5(LCP1):​c.-25+1512A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0492 in 152,288 control chromosomes in the GnomAD database, including 296 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 0.049 ( 296 hom., cov: 32)

Consequence

LCP1
NM_002298.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0170
Variant links:
Genes affected
LCP1 (HGNC:6528): (lymphocyte cytosolic protein 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. Plastin 1 (otherwise known as Fimbrin) is a third distinct plastin isoform which is specifically expressed at high levels in the small intestine. The L isoform is expressed only in hemopoietic cell lineages, while the T isoform has been found in all other normal cells of solid tissues that have replicative potential (fibroblasts, endothelial cells, epithelial cells, melanocytes, etc.). However, L-plastin has been found in many types of malignant human cells of non-hemopoietic origin suggesting that its expression is induced accompanying tumorigenesis in solid tissues. [provided by RefSeq, Jul 2008]

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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=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LCP1NM_002298.5 linkuse as main transcriptc.-25+1512A>G intron_variant ENST00000323076.7 NP_002289.2 P13796-1A0A024RDT4
LCP1XM_005266374.3 linkuse as main transcriptc.-12161A>G 5_prime_UTR_premature_start_codon_gain_variant 1/16 XP_005266431.1 P13796-1A0A024RDT4
LCP1XM_005266374.3 linkuse as main transcriptc.-12161A>G 5_prime_UTR_variant 1/16 XP_005266431.1 P13796-1A0A024RDT4
LCP1XM_047430305.1 linkuse as main transcriptc.-25+1512A>G intron_variant XP_047286261.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LCP1ENST00000323076.7 linkuse as main transcriptc.-25+1512A>G intron_variant 1 NM_002298.5 ENSP00000315757.2 P13796-1
LCP1ENST00000398576.6 linkuse as main transcriptc.-25+1512A>G intron_variant 5 ENSP00000381581.1 P13796-1
LCP1ENST00000442275.1 linkuse as main transcriptc.-25+1512A>G intron_variant 3 ENSP00000402157.1 Q5TBN5
LCP1ENST00000460190.1 linkuse as main transcriptn.94+1512A>G intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0490
AC:
7456
AN:
152170
Hom.:
291
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.110
Gnomad AMI
AF:
0.00219
Gnomad AMR
AF:
0.0263
Gnomad ASJ
AF:
0.0634
Gnomad EAS
AF:
0.0517
Gnomad SAS
AF:
0.0753
Gnomad FIN
AF:
0.0143
Gnomad MID
AF:
0.0633
Gnomad NFE
AF:
0.0203
Gnomad OTH
AF:
0.0483
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0492
AC:
7488
AN:
152288
Hom.:
296
Cov.:
32
AF XY:
0.0487
AC XY:
3629
AN XY:
74482
show subpopulations
Gnomad4 AFR
AF:
0.110
Gnomad4 AMR
AF:
0.0263
Gnomad4 ASJ
AF:
0.0634
Gnomad4 EAS
AF:
0.0511
Gnomad4 SAS
AF:
0.0752
Gnomad4 FIN
AF:
0.0143
Gnomad4 NFE
AF:
0.0203
Gnomad4 OTH
AF:
0.0544
Alfa
AF:
0.0338
Hom.:
86
Bravo
AF:
0.0507

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
4.4
DANN
Benign
0.75

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs9567638; hg19: chr13-46754734; API