Variant 14-93721486-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_178013.4(PRIMA1):c.420G>A(p.Ser140=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 1,612,388 control chromosomes in the GnomAD database, including 323,011 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.58 ( 26673 hom., cov: 31)

Exomes 𝑓: 0.63 ( 296338 hom. )

Consequence

PRIMA1
NM_178013.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

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]

PRIMA1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 14-93721486-C-T is Benign according to our data. Variant chr14-93721486-C-T is described in ClinVar as [Benign]. Clinvar id is 586377.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.83 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRIMA1	NM_178013.4 linkuse as main transcript	c.420G>A	p.Ser140=	synonymous_variant	5/5	ENST00000393140.6	NP_821092.1
PRIMA1	XM_011536456.3 linkuse as main transcript	c.420G>A	p.Ser140=	synonymous_variant	5/5		XP_011534758.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRIMA1	ENST00000393140.6 linkuse as main transcript	c.420G>A	p.Ser140=	synonymous_variant	5/5	1	NM_178013.4	ENSP00000376848	P1	Q86XR5-1
PRIMA1	ENST00000393143.5 linkuse as main transcript	c.420G>A	p.Ser140=	synonymous_variant	4/4	1		ENSP00000376851	P1	Q86XR5-1
PRIMA1	ENST00000316227.3 linkuse as main transcript	c.*216G>A		3_prime_UTR_variant	5/5	1		ENSP00000320948		Q86XR5-2
PRIMA1	ENST00000477603.5 linkuse as main transcript	c.*216G>A		3_prime_UTR_variant, NMD_transcript_variant	6/6	1		ENSP00000434370		Q86XR5-2

Frequencies

GnomAD3 genomes

AF:

0.582

AC:

88386

AN:

151830

Hom.:

26667

Cov.:

show subpopulations

Gnomad AFR

AF:

0.428

Gnomad AMI

AF:

0.620

Gnomad AMR

AF:

0.671

Gnomad ASJ

AF:

0.725

Gnomad EAS

AF:

0.341

Gnomad SAS

AF:

0.546

Gnomad FIN

AF:

0.636

Gnomad MID

AF:

0.671

Gnomad NFE

AF:

0.659

Gnomad OTH

AF:

0.610

GnomAD3 exomes

AF:

0.607

AC:

152360

AN:

251012

Hom.:

47664

AF XY:

0.610

AC XY:

82765

AN XY:

135652

show subpopulations

Gnomad AFR exome

AF:

0.419

Gnomad AMR exome

AF:

0.668

Gnomad ASJ exome

AF:

0.728

Gnomad EAS exome

AF:

0.328

Gnomad SAS exome

AF:

0.553

Gnomad FIN exome

AF:

0.632

Gnomad NFE exome

AF:

0.658

Gnomad OTH exome

AF:

0.630

GnomAD4 exome

AF:

0.633

AC:

924802

AN:

1460440

Hom.:

296338

Cov.:

AF XY:

0.632

AC XY:

459312

AN XY:

726606

show subpopulations

Gnomad4 AFR exome

AF:

0.419

Gnomad4 AMR exome

AF:

0.667

Gnomad4 ASJ exome

AF:

0.725

Gnomad4 EAS exome

AF:

0.349

Gnomad4 SAS exome

AF:

0.550

Gnomad4 FIN exome

AF:

0.629

Gnomad4 NFE exome

AF:

0.654

Gnomad4 OTH exome

AF:

0.618

GnomAD4 genome

AF:

0.582

AC:

88431

AN:

151948

Hom.:

26673

Cov.:

AF XY:

0.583

AC XY:

43262

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.428

Gnomad4 AMR

AF:

0.671

Gnomad4 ASJ

AF:

0.725

Gnomad4 EAS

AF:

0.342

Gnomad4 SAS

AF:

0.547

Gnomad4 FIN

AF:

0.636

Gnomad4 NFE

AF:

0.659

Gnomad4 OTH

AF:

0.603

Alfa

AF:

0.648

Hom.:

57678

Bravo

AF:

0.577

Asia WGS

AF:

0.445

AC:

1555

AN:

3478

EpiCase

AF:

0.666

EpiControl

AF:

0.666

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 20, 2017	- -

Sleep-related hypermotor epilepsy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

0.13

DANN

Benign

0.61

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over