chr9-15483213-A-G

Position:

• chr9-15483213-A-G

Variant summary

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

The NM_033222.5(PSIP1):​c.456+2793T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 151,954 control chromosomes in the GnomAD database, including 38,788 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 0.69 (38788 hom., cov: 30)
• Consequence: PSIP1 NM_033222.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSIP1	NM_033222.5	c.456+2793T>C		intron_variant		ENST00000380733.9	NP_150091.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSIP1	ENST00000380733.9	c.456+2793T>C		intron_variant		1	NM_033222.5	ENSP00000370109	P1

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104198 AN: 151836 Hom.: 38771 Cov.: 30

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.686 AC: 104231 AN: 151954 Hom.: 38788 Cov.: 30 AF XY: 0.686 AC XY: 50926 AN XY: 74288

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.719

Alfa AF: 0.794 Hom.: 45618

Bravo AF: 0.679

Asia WGS AF: 0.660 AC: 2296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.45

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: rs1033056; hg19: chr9-15483211;