rs10962048

chr9-15507810-C-G

Variant summary

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

The NM_033222.5(PSIP1):c.73-1173G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 152,222 control chromosomes in the GnomAD database, including 632 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 0.084 (632 hom., cov: 33)
• Consequence: PSIP1 NM_033222.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSIP1	NM_033222.5	c.73-1173G>C		intron_variant		ENST00000380733.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSIP1	ENST00000380733.9	c.73-1173G>C		intron_variant		1	NM_033222.5	P1

Frequencies

GnomAD3 genomes AF: 0.0837 AC: 12732 AN: 152104 Hom.: 622 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0632

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0534

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0838 AC: 12763 AN: 152222 Hom.: 632 Cov.: 33 AF XY: 0.0854 AC XY: 6354 AN XY: 74420

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0632

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0624

Gnomad4 NFE AF: 0.0534

Gnomad4 OTH AF: 0.0753

Alfa AF: 0.0673 Hom.: 62

Bravo AF: 0.0836

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.24
Dann	Benign	0.59

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: rs10962048; hg19: chr9-15507808;