9-15509368-G-C

Variant names:

• chr9-15509368-G-C
• rs7470146
• NM_033222.5:c.72+749C>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_033222.5(PSIP1):​c.72+749C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,990 control chromosomes in the GnomAD database, including 11,248 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 0.34 (11248 hom., cov: 32)
• Consequence: PSIP1 NM_033222.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 3 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 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.72+749C>G		intron	N/A	NP_150091.2
	PSIP1	NM_001128217.3		c.72+749C>G		intron	N/A	NP_001121689.1
	PSIP1	NM_001438383.1		c.72+749C>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.72+749C>G		intron	N/A	ENSP00000370109.4
	PSIP1	ENST00000380738.8	TSL:1	c.72+749C>G		intron	N/A	ENSP00000370114.4
	PSIP1	ENST00000397519.6	TSL:1	c.72+749C>G		intron	N/A	ENSP00000380653.2

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52132 AN: 151872 Hom.: 11244 Cov.: 32

Gnomad AFR AF: 0.0832

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.343 AC: 52135 AN: 151990 Hom.: 11248 Cov.: 32 AF XY: 0.354 AC XY: 26293 AN XY: 74268

African (AFR) AF: 0.0830 AC: 3445 AN: 41504

American (AMR) AF: 0.499 AC: 7612 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3468

East Asian (EAS) AF: 0.692 AC: 3571 AN: 5162

South Asian (SAS) AF: 0.378 AC: 1825 AN: 4822

European-Finnish (FIN) AF: 0.532 AC: 5589 AN: 10510

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27618 AN: 67952

Other (OTH) AF: 0.383 AC: 809 AN: 2112

Alfa AF: 0.257 Hom.: 782

Bravo AF: 0.337

Asia WGS AF: 0.454 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.37
DANN	Benign	0.42
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.35		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.35		Position offset: 1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7470146; hg19: chr9-15509366; COSMIC: COSV66255556;