9-15498497-C-T

Variant names:

• chr9-15498497-C-T
• rs12339417
• NM_033222.5:c.149+8064G>A

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+8064G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 150,920 control chromosomes in the GnomAD database, including 8,299 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 0.25 (8299 hom., cov: 31)
• Consequence: PSIP1 NM_033222.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.55
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSIP1	NM_033222.5	c.149+8064G>A		intron_variant	Intron 3 of 15	ENST00000380733.9	NP_150091.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSIP1	ENST00000380733.9	c.149+8064G>A		intron_variant	Intron 3 of 15	1	NM_033222.5	ENSP00000370109.4

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37671 AN: 150802 Hom.: 8262 Cov.: 31

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.250 AC: 37761 AN: 150920 Hom.: 8299 Cov.: 31 AF XY: 0.247 AC XY: 18185 AN XY: 73600

African (AFR) AF: 0.599 AC: 24646 AN: 41114

American (AMR) AF: 0.149 AC: 2265 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 578 AN: 3464

East Asian (EAS) AF: 0.100 AC: 515 AN: 5144

South Asian (SAS) AF: 0.201 AC: 963 AN: 4790

European-Finnish (FIN) AF: 0.0925 AC: 941 AN: 10174

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.107 AC: 7270 AN: 67768

Other (OTH) AF: 0.231 AC: 482 AN: 2090

Alfa AF: 0.106 Hom.: 357

Bravo AF: 0.266

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.56
PhyloP100		-4.6
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: rs12339417; hg19: chr9-15498495;