rs10119931

chr9-15495080-A-C

Variant summary

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

The NM_033222.5(PSIP1):c.150-4956T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0892 in 152,200 control chromosomes in the GnomAD database, including 990 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 0.089 (990 hom., cov: 32)
• Consequence: PSIP1 NM_033222.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSIP1	NM_033222.5	c.150-4956T>G		intron_variant		ENST00000380733.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSIP1	ENST00000380733.9	c.150-4956T>G		intron_variant		1	NM_033222.5	P1

Frequencies

GnomAD3 genomes AF: 0.0891 AC: 13553 AN: 152082 Hom.: 988 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0609

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.00500

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.0237

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0495

Gnomad OTH AF: 0.0966

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

GnomAD4 genome AF: 0.0892 AC: 13571 AN: 152200 Hom.: 990 Cov.: 32 AF XY: 0.0863 AC XY: 6426 AN XY: 74434

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.0607

Gnomad4 ASJ AF: 0.0813

Gnomad4 EAS AF: 0.00501

Gnomad4 SAS AF: 0.0331

Gnomad4 FIN AF: 0.0237

Gnomad4 NFE AF: 0.0495

Gnomad4 OTH AF: 0.0965

Alfa AF: 0.0781 Hom.: 163

Bravo AF: 0.0969

Asia WGS AF: 0.0430 AC: 149 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.3
Dann	Benign	0.60

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: rs10119931; hg19: chr9-15495078;