rs10119931

Variant names:

• chr9-15495080-A-C
• rs10119931
• NM_033222.5:c.150-4956T>G

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 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.150-4956T>G		intron	N/A	NP_150091.2
	PSIP1	NM_001128217.3		c.150-4956T>G		intron	N/A	NP_001121689.1
	PSIP1	NM_001438383.1		c.150-4956T>G		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.150-4956T>G		intron	N/A	ENSP00000370109.4
	PSIP1	ENST00000380738.8	TSL:1	c.150-4956T>G		intron	N/A	ENSP00000370114.4
	PSIP1	ENST00000397519.6	TSL:1	c.150-4956T>G		intron	N/A	ENSP00000380653.2

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

African (AFR) AF: 0.200 AC: 8286 AN: 41496

American (AMR) AF: 0.0607 AC: 928 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 282 AN: 3470

East Asian (EAS) AF: 0.00501 AC: 26 AN: 5190

South Asian (SAS) AF: 0.0331 AC: 160 AN: 4828

European-Finnish (FIN) AF: 0.0237 AC: 251 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0495 AC: 3366 AN: 68004

Other (OTH) AF: 0.0965 AC: 204 AN: 2114

Alfa AF: 0.0844 Hom.: 196

Bravo AF: 0.0969

Asia WGS AF: 0.0430 AC: 149 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.60
PhyloP100		0.077
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: rs10119931; hg19: chr9-15495078;