14-93721486-C-G

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_178013.4(PRIMA1):​c.420G>C​(p.Ser140Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Consequence

PRIMA1
NM_178013.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.83
Variant links:
Genes affected
PRIMA1 (HGNC:18319): (proline rich membrane anchor 1) The product of this gene functions to organize acetylcholinesterase (AChE) into tetramers, and to anchor AChE at neural cell membranes. [provided by RefSeq, Nov 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP7
Synonymous conserved (PhyloP=-1.83 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PRIMA1NM_178013.4 linkuse as main transcriptc.420G>C p.Ser140Ser synonymous_variant 5/5 ENST00000393140.6 NP_821092.1 Q86XR5-1A0A024R6J9
PRIMA1XM_011536456.3 linkuse as main transcriptc.420G>C p.Ser140Ser synonymous_variant 5/5 XP_011534758.1 Q86XR5-1A0A024R6J9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PRIMA1ENST00000393140.6 linkuse as main transcriptc.420G>C p.Ser140Ser synonymous_variant 5/51 NM_178013.4 ENSP00000376848.1 Q86XR5-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
41
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
0.10
DANN
Benign
0.52

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: rs1887197; hg19: chr14-94187832; API