chr9-15500152-C-G

Variant names:

• chr9-15500152-C-G
• rs10283923
• NM_033222.5:c.149+6409G>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.149+6409G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,116 control chromosomes in the GnomAD database, including 5,771 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 0.22 (5771 hom., cov: 32)
• Consequence: PSIP1 NM_033222.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 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.149+6409G>C		intron	N/A	NP_150091.2
	PSIP1	NM_001128217.3		c.149+6409G>C		intron	N/A	NP_001121689.1
	PSIP1	NM_001438383.1		c.149+6409G>C		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.149+6409G>C		intron	N/A	ENSP00000370109.4
	PSIP1	ENST00000380738.8	TSL:1	c.149+6409G>C		intron	N/A	ENSP00000370114.4
	PSIP1	ENST00000397519.6	TSL:1	c.149+6409G>C		intron	N/A	ENSP00000380653.2

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33088 AN: 151998 Hom.: 5741 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.218 AC: 33169 AN: 152116 Hom.: 5771 Cov.: 32 AF XY: 0.216 AC XY: 16059 AN XY: 74378

African (AFR) AF: 0.487 AC: 20204 AN: 41464

American (AMR) AF: 0.134 AC: 2047 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 644 AN: 3468

East Asian (EAS) AF: 0.100 AC: 519 AN: 5168

South Asian (SAS) AF: 0.201 AC: 970 AN: 4822

European-Finnish (FIN) AF: 0.0898 AC: 950 AN: 10578

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7302 AN: 68016

Other (OTH) AF: 0.203 AC: 428 AN: 2112

Alfa AF: 0.0607 Hom.: 76

Bravo AF: 0.230

Asia WGS AF: 0.191 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.26
PhyloP100		-0.15
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: rs10283923; hg19: chr9-15500150;