9-15486723-G-A

Variant names:

• chr9-15486723-G-A
• rs2737829
• NM_033222.5:c.393+104C>T

Variant summary

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

The NM_033222.5(PSIP1):​c.393+104C>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: PSIP1 NM_033222.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486
• Publications: 6 publications found

Genes affected

PSIP1 (HGNC:9527): (PC4 and SRSF1 interacting protein 1) Enables DNA-binding transcription factor binding activity; chromatin binding activity; and transcription coactivator activity. Involved in mRNA 5'-splice site recognition and positive regulation of transcription by RNA polymerase II. Located in heterochromatin; nuclear periphery; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033222.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSIP1	NM_033222.5	MANE Select	c.393+104C>T		intron	N/A	NP_150091.2
	PSIP1	NM_001128217.3		c.393+104C>T		intron	N/A	NP_001121689.1
	PSIP1	NM_001438383.1		c.393+104C>T		intron	N/A	NP_001425312.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSIP1	ENST00000380733.9	TSL:1 MANE Select	c.393+104C>T		intron	N/A	ENSP00000370109.4
	PSIP1	ENST00000380738.8	TSL:1	c.393+104C>T		intron	N/A	ENSP00000370114.4
	PSIP1	ENST00000397519.6	TSL:1	c.393+104C>T		intron	N/A	ENSP00000380653.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 644778 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 345236

African (AFR) AF: 0.00 AC: 0 AN: 14414

American (AMR) AF: 0.00 AC: 0 AN: 22892

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18804

East Asian (EAS) AF: 0.00 AC: 0 AN: 32516

South Asian (SAS) AF: 0.00 AC: 0 AN: 57268

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44236

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2506

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 419396

Other (OTH) AF: 0.00 AC: 0 AN: 32746

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 2825

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.75
DANN	Benign	0.88
PhyloP100		-0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2737829; hg19: chr9-15486721;