rs17337140

Variant names:

• chr9-15481192-G-A
• rs17337140
• NM_033222.5:c.457-1505C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033222.5(PSIP1):​c.457-1505C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0733 in 152,208 control chromosomes in the GnomAD database, including 578 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 0.073 (578 hom., cov: 32)
• Consequence: PSIP1 NM_033222.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 1 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 = 0.112 is higher than 0.05.

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.457-1505C>T		intron	N/A	NP_150091.2
	PSIP1	NM_001128217.3		c.457-1505C>T		intron	N/A	NP_001121689.1
	PSIP1	NM_001438383.1		c.457-1505C>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.457-1505C>T		intron	N/A	ENSP00000370109.4
	PSIP1	ENST00000380738.8	TSL:1	c.457-1505C>T		intron	N/A	ENSP00000370114.4
	PSIP1	ENST00000397519.6	TSL:1	c.457-1505C>T		intron	N/A	ENSP00000380653.2

Frequencies

GnomAD3 genomes AF: 0.0733 AC: 11149 AN: 152090 Hom.: 578 Cov.: 32

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.0733

Gnomad ASJ AF: 0.0729

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.0215

Gnomad FIN AF: 0.0570

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0875

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

GnomAD4 genome AF: 0.0733 AC: 11150 AN: 152208 Hom.: 578 Cov.: 32 AF XY: 0.0692 AC XY: 5148 AN XY: 74420

African (AFR) AF: 0.0188 AC: 780 AN: 41540

American (AMR) AF: 0.0733 AC: 1120 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0729 AC: 253 AN: 3470

East Asian (EAS) AF: 0.00386 AC: 20 AN: 5180

South Asian (SAS) AF: 0.0211 AC: 102 AN: 4826

European-Finnish (FIN) AF: 0.0570 AC: 603 AN: 10588

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7751 AN: 68006

Other (OTH) AF: 0.0866 AC: 183 AN: 2114

Alfa AF: 0.0977 Hom.: 171

Bravo AF: 0.0752

Asia WGS AF: 0.0260 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.34
PhyloP100		-0.099
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: rs17337140; hg19: chr9-15481190;