Variant rs4905087 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_178013.4(PRIMA1):c.102T>C(p.His34His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 1,546,064 control chromosomes in the GnomAD database, including 437,153 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.71 ( 38596 hom., cov: 27)

Exomes 𝑓: 0.75 ( 398557 hom. )

Consequence

PRIMA1
NM_178013.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -1.16

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 14-93779303-A-G is Benign according to our data. Variant chr14-93779303-A-G is described in ClinVar as [Benign]. Clinvar id is 586376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.767 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.102T>C	p.His34His	synonymous_variant	3/5	ENST00000393140.6	NP_821092.1	Q86XR5-1A0A024R6J9
PRIMA1	XM_011536456.3 linkuse as main transcript	c.102T>C	p.His34His	synonymous_variant	3/5		XP_011534758.1	Q86XR5-1A0A024R6J9
PRIMA1	XM_047430966.1 linkuse as main transcript	c.102T>C	p.His34His	synonymous_variant	3/5		XP_047286922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PRIMA1	ENST00000393140.6 linkuse as main transcript	c.102T>C	p.His34His	synonymous_variant	3/5	1	NM_178013.4	ENSP00000376848.1	Q86XR5-1
PRIMA1	ENST00000393143.5 linkuse as main transcript	c.102T>C	p.His34His	synonymous_variant	2/4	1		ENSP00000376851.1	Q86XR5-1
PRIMA1	ENST00000316227.3 linkuse as main transcript	c.102T>C	p.His34His	synonymous_variant	2/5	1		ENSP00000320948.3	Q86XR5-2
PRIMA1	ENST00000477603.5 linkuse as main transcript	n.102T>C		non_coding_transcript_exon_variant	3/6	1		ENSP00000434370.1	Q86XR5-2

Frequencies

GnomAD3 genomes

AF:

0.708

AC:

106910

AN:

151040

Hom.:

38563

Cov.:

show subpopulations

Gnomad AFR

AF:

0.638

Gnomad AMI

AF:

0.823

Gnomad AMR

AF:

0.688

Gnomad ASJ

AF:

0.764

Gnomad EAS

AF:

0.322

Gnomad SAS

AF:

0.602

Gnomad FIN

AF:

0.797

Gnomad MID

AF:

0.747

Gnomad NFE

AF:

0.773

Gnomad OTH

AF:

0.703

GnomAD3 exomes

AF:

0.686

AC:

130850

AN:

190836

Hom.:

46652

AF XY:

0.692

AC XY:

73150

AN XY:

105656

show subpopulations

Gnomad AFR exome

AF:

0.622

Gnomad AMR exome

AF:

0.606

Gnomad ASJ exome

AF:

0.763

Gnomad EAS exome

AF:

0.266

Gnomad SAS exome

AF:

0.605

Gnomad FIN exome

AF:

0.789

Gnomad NFE exome

AF:

0.762

Gnomad OTH exome

AF:

0.714

GnomAD4 exome

AF:

0.750

AC:

1046514

AN:

1394906

Hom.:

398557

Cov.:

AF XY:

0.748

AC XY:

517787

AN XY:

692360

show subpopulations

Gnomad4 AFR exome

AF:

0.623

Gnomad4 AMR exome

AF:

0.613

Gnomad4 ASJ exome

AF:

0.768

Gnomad4 EAS exome

AF:

0.340

Gnomad4 SAS exome

AF:

0.627

Gnomad4 FIN exome

AF:

0.788

Gnomad4 NFE exome

AF:

0.778

Gnomad4 OTH exome

AF:

0.730

GnomAD4 genome

AF:

0.708

AC:

106987

AN:

151158

Hom.:

38596

Cov.:

AF XY:

0.706

AC XY:

52113

AN XY:

73818

show subpopulations

Gnomad4 AFR

AF:

0.638

Gnomad4 AMR

AF:

0.687

Gnomad4 ASJ

AF:

0.764

Gnomad4 EAS

AF:

0.322

Gnomad4 SAS

AF:

0.603

Gnomad4 FIN

AF:

0.797

Gnomad4 NFE

AF:

0.773

Gnomad4 OTH

AF:

0.697

Alfa

AF:

0.739

Hom.:

12358

Bravo

AF:

0.696

Asia WGS

AF:

0.499

AC:

1732

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 20, 2017	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 09, 2021	- -

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

-0.77

CADD

Benign

0.94

DANN

Benign

0.30

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

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