9-15483213-A-G

Variant names:

• chr9-15483213-A-G
• rs1033056
• NM_033222.5:c.456+2793T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
PSIP1	NM_033222.5	c.456+2793T>C		intron_variant	Intron 6 of 15	ENST00000380733.9	NP_150091.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSIP1	ENST00000380733.9	c.456+2793T>C		intron_variant	Intron 6 of 15	1	NM_033222.5	ENSP00000370109.4

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

African (AFR) AF: 0.372 AC: 15384 AN: 41396

American (AMR) AF: 0.811 AC: 12367 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2588 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3911 AN: 5170

South Asian (SAS) AF: 0.597 AC: 2871 AN: 4812

European-Finnish (FIN) AF: 0.813 AC: 8596 AN: 10572

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55931 AN: 67962

Other (OTH) AF: 0.719 AC: 1518 AN: 2110

Alfa AF: 0.777 Hom.: 58560

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
PhyloP100		-0.58
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: rs1033056; hg19: chr9-15483211;