rs7698829

Variant names:

• chr4-154540315-C-A
• rs7698829
• NM_002669.4:c.940-262G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-154540315-C-A
• chr4-154540315-C-G
• chr4-154540315-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002669.4(PLRG1):​c.940-262G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PLRG1 NM_002669.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.49
• Publications: 3 publications found

Genes affected

PLRG1 (HGNC:9089): (pleiotropic regulator 1) This gene encodes a core component of the cell division cycle 5-like (CDC5L) complex. The CDC5L complex is part of the spliceosome and is required for pre-mRNA splicing. The encoded protein plays a critical role in alternative splice site selection. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLRG1	NM_002669.4	c.940-262G>T		intron_variant	Intron 10 of 14	ENST00000499023.7	NP_002660.1
PLRG1	NM_001201564.2	c.913-262G>T		intron_variant	Intron 10 of 14		NP_001188493.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLRG1	ENST00000499023.7	c.940-262G>T		intron_variant	Intron 10 of 14	1	NM_002669.4	ENSP00000424417.1
PLRG1	ENST00000302078.9	c.913-262G>T		intron_variant	Intron 10 of 14	1		ENSP00000303191.5
PLRG1	ENST00000506627.5	n.253-262G>T		intron_variant	Intron 2 of 6	5		ENSP00000425914.1
PLRG1	ENST00000507125.1	n.-43G>T		upstream_gene_variant		3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 422932 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 222370

African (AFR) AF: 0.00 AC: 0 AN: 11908

American (AMR) AF: 0.00 AC: 0 AN: 15088

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13270

East Asian (EAS) AF: 0.00 AC: 0 AN: 30222

South Asian (SAS) AF: 0.00 AC: 0 AN: 38326

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28958

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1896

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 258404

Other (OTH) AF: 0.00 AC: 0 AN: 24860

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.63
DANN	Benign	0.64
PhyloP100		-3.5

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: rs7698829; hg19: chr4-155461467;