2-178432255-C-CTATATCCAAATATGTTATATTAAAACCT

Variant names:

• chr2-178432255-C-CTATATCCAAATATGTTATATTAAAACCT
• rs751875722
• NM_003690.5:c.785-2_785-1insAGGTTTTAATATAACATATTTGGATATA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_003690.5(PRKRA):​c.785-2_785-1insAGGTTTTAATATAACATATTTGGATATA variant causes a splice acceptor, intron change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 35)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PRKRA NM_003690.5 splice_acceptor, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.98
• Publications: 0 publications found

Genes affected

PRKRA (HGNC:9438): (protein activator of interferon induced protein kinase EIF2AK2) This gene encodes a protein kinase activated by double-stranded RNA which mediates the effects of interferon in response to viral infection. Mutations in this gene have been associated with dystonia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2008]

CHROMR (HGNC:54059): (cholesterol induced regulator of metabolism RNA)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003690.5. 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
	PRKRA	NM_003690.5	MANE Select	c.785-2_785-1insAGGTTTTAATATAACATATTTGGATATA		splice_acceptor intron	N/A	NP_003681.1	O75569-1
	PRKRA	NM_001139517.1		c.752-2_752-1insAGGTTTTAATATAACATATTTGGATATA		splice_acceptor intron	N/A	NP_001132989.1	O75569-2
	PRKRA	NM_001139518.1		c.710-2_710-1insAGGTTTTAATATAACATATTTGGATATA		splice_acceptor intron	N/A	NP_001132990.1	O75569-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRKRA	ENST00000325748.9	TSL:1 MANE Select	c.785-2_785-1insAGGTTTTAATATAACATATTTGGATATA		splice_acceptor intron	N/A	ENSP00000318176.4	O75569-1
	PRKRA	ENST00000432031.6	TSL:1	c.752-2_752-1insAGGTTTTAATATAACATATTTGGATATA		splice_acceptor intron	N/A	ENSP00000393883.2	O75569-2
	PRKRA	ENST00000487082.5	TSL:1	c.710-2_710-1insAGGTTTTAATATAACATATTTGGATATA		splice_acceptor intron	N/A	ENSP00000430604.1	O75569-3

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1461824 Hom.: 0 Cov.: 56 AF XY: 0.00 AC XY: 0 AN XY: 727220

African (AFR) AF: 0.00 AC: 0 AN: 33478

American (AMR) AF: 0.00 AC: 0 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39694

South Asian (SAS) AF: 0.00 AC: 0 AN: 86256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53414

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1111966

Other (OTH) AF: 0.00 AC: 0 AN: 60394

GnomAD4 genome Cov.: 35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs751875722; hg19: chr2-179296982;