14-93738999-G-A

Position:

• chr14-93738999-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178013.4(PRIMA1):​c.230-1629C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,118 control chromosomes in the GnomAD database, including 53,808 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 0.84 (53808 hom., cov: 32)
• Consequence: PRIMA1 NM_178013.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRIMA1	NM_178013.4	c.230-1629C>T		intron_variant		ENST00000393140.6	NP_821092.1
PRIMA1	XM_011536456.3	c.230-1629C>T		intron_variant			XP_011534758.1
PRIMA1	XM_047430966.1	c.230-1629C>T		intron_variant			XP_047286922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRIMA1	ENST00000393140.6	c.230-1629C>T		intron_variant		1	NM_178013.4	ENSP00000376848.1
PRIMA1	ENST00000393143.5	c.230-1629C>T		intron_variant		1		ENSP00000376851.1
PRIMA1	ENST00000316227.3	c.230-1629C>T		intron_variant		1		ENSP00000320948.3
PRIMA1	ENST00000477603.5	n.230-1629C>T		intron_variant		1		ENSP00000434370.1

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127035 AN: 152002 Hom.: 53779 Cov.: 32

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.855

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.836 AC: 127113 AN: 152118 Hom.: 53808 Cov.: 32 AF XY: 0.833 AC XY: 61913 AN XY: 74356

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.880

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.882

Gnomad4 NFE AF: 0.905

Gnomad4 OTH AF: 0.848

Alfa AF: 0.887 Hom.: 99129

Bravo AF: 0.831

Asia WGS AF: 0.641 AC: 2228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.80
DANN	Benign	0.31

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: rs6575353; hg19: chr14-94205345;