rs6575353

Variant names:

• chr14-93738999-G-A
• rs6575353
• NM_178013.4:c.230-1629C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-93738999-G-A
• chr14-93738999-G-C
• chr14-93738999-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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 Gene-Disease associations (from GenCC):

• epilepsy

  Inheritance: AR Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178013.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRIMA1	NM_178013.4	MANE Select	c.230-1629C>T		intron	N/A	NP_821092.1	Q86XR5-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRIMA1	ENST00000393140.6	TSL:1 MANE Select	c.230-1629C>T		intron	N/A	ENSP00000376848.1	Q86XR5-1
	PRIMA1	ENST00000393143.5	TSL:1	c.230-1629C>T		intron	N/A	ENSP00000376851.1	Q86XR5-1
	PRIMA1	ENST00000316227.3	TSL:1	c.230-1629C>T		intron	N/A	ENSP00000320948.3	Q86XR5-2

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

African (AFR) AF: 0.737 AC: 30534 AN: 41452

American (AMR) AF: 0.880 AC: 13467 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2948 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2506 AN: 5174

South Asian (SAS) AF: 0.799 AC: 3857 AN: 4826

European-Finnish (FIN) AF: 0.882 AC: 9318 AN: 10566

Middle Eastern (MID) AF: 0.914 AC: 267 AN: 292

European-Non Finnish (NFE) AF: 0.905 AC: 61535 AN: 68014

Other (OTH) AF: 0.848 AC: 1790 AN: 2110

Alfa AF: 0.876 Hom.: 236573

Bravo AF: 0.831

Asia WGS AF: 0.641 AC: 2228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.80
DANN	Benign	0.31
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6575353; hg19: chr14-94205345;