chr9-15507810-C-G

Variant names:

• chr9-15507810-C-G
• rs10962048
• NM_033222.5:c.73-1173G>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.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
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.134 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSIP1	NM_033222.5	MANE Select	c.73-1173G>C		intron	N/A	NP_150091.2
	PSIP1	NM_001128217.3		c.73-1173G>C		intron	N/A	NP_001121689.1	O75475-1
	PSIP1	NM_001438383.1		c.73-1173G>C		intron	N/A	NP_001425312.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSIP1	ENST00000380733.9	TSL:1 MANE Select	c.73-1173G>C		intron	N/A	ENSP00000370109.4	O75475-1
	PSIP1	ENST00000380738.8	TSL:1	c.73-1173G>C		intron	N/A	ENSP00000370114.4	O75475-1
	PSIP1	ENST00000397519.6	TSL:1	c.73-1173G>C		intron	N/A	ENSP00000380653.2	O75475-2

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

African (AFR) AF: 0.137 AC: 5693 AN: 41528

American (AMR) AF: 0.0632 AC: 967 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3470

East Asian (EAS) AF: 0.114 AC: 593 AN: 5184

South Asian (SAS) AF: 0.138 AC: 664 AN: 4818

European-Finnish (FIN) AF: 0.0624 AC: 661 AN: 10600

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0534 AC: 3631 AN: 68010

Other (OTH) AF: 0.0753 AC: 159 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.59
PhyloP100		-0.66
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: rs10962048; hg19: chr9-15507808;