9-15488818-G-A

Variant names:

• chr9-15488818-G-A
• rs2737839
• NM_033222.5:c.288+1168C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_033222.5(PSIP1):​c.288+1168C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 152,176 control chromosomes in the GnomAD database, including 20 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 0.016 (20 hom., cov: 32)
• Consequence: PSIP1 NM_033222.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 0 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=-0.86).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0155 (2360/152176) while in subpopulation AFR AF = 0.0345 (1433/41488). AF 95% confidence interval is 0.0331. There are 20 homozygotes in GnomAd4. There are 1174 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High AC in GnomAd4 at 2360 AD gene.

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.288+1168C>T		intron	N/A	NP_150091.2
	PSIP1	NM_001128217.3		c.288+1168C>T		intron	N/A	NP_001121689.1
	PSIP1	NM_001438383.1		c.288+1168C>T		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.288+1168C>T		intron	N/A	ENSP00000370109.4
	PSIP1	ENST00000380738.8	TSL:1	c.288+1168C>T		intron	N/A	ENSP00000370114.4
	PSIP1	ENST00000397519.6	TSL:1	c.288+1168C>T		intron	N/A	ENSP00000380653.2

Frequencies

GnomAD3 genomes AF: 0.0155 AC: 2359 AN: 152058 Hom.: 20 Cov.: 32

Gnomad AFR AF: 0.0346

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0105

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.00498

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00954

Gnomad OTH AF: 0.0182

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

GnomAD4 genome AF: 0.0155 AC: 2360 AN: 152176 Hom.: 20 Cov.: 32 AF XY: 0.0158 AC XY: 1174 AN XY: 74402

African (AFR) AF: 0.0345 AC: 1433 AN: 41488

American (AMR) AF: 0.0105 AC: 160 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5170

South Asian (SAS) AF: 0.00477 AC: 23 AN: 4820

European-Finnish (FIN) AF: 0.00283 AC: 30 AN: 10612

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00954 AC: 649 AN: 68004

Other (OTH) AF: 0.0180 AC: 38 AN: 2106

Alfa AF: 0.00259 Hom.: 0

Bravo AF: 0.0172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.97
PhyloP100		-0.27
Mutation Taster		=100/0	polymorphism

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: rs2737839; hg19: chr9-15488816; COSMIC: COSV66253946; COSMIC: COSV66253946;