rs9288125

Variant names:

• chr2-152666597-A-C
• rs9288125
• NM_001365597.4:c.1891-2345T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-152666597-A-C
• chr2-152666597-A-G
• chr2-152666597-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001365597.4(PRPF40A):​c.1891-2345T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,016 control chromosomes in the GnomAD database, including 48,085 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 0.79 (48085 hom., cov: 31)
• Consequence: PRPF40A NM_001365597.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547
• Publications: 4 publications found

Genes affected

PRPF40A (HGNC:16463): (pre-mRNA processing factor 40 homolog A) Enables RNA binding activity. Involved in several processes, including cytoskeleton organization; regulation of cell shape; and regulation of cytokinesis. Located in nuclear matrix and nuclear speck. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRPF40A	NM_001365597.4	c.1891-2345T>G		intron_variant	Intron 16 of 25	ENST00000545856.8	NP_001352526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRPF40A	ENST00000545856.8	c.1891-2345T>G		intron_variant	Intron 16 of 25	1	NM_001365597.4	ENSP00000444656.4

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120427 AN: 151898 Hom.: 48062 Cov.: 31

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.793 AC: 120501 AN: 152016 Hom.: 48085 Cov.: 31 AF XY: 0.794 AC XY: 59013 AN XY: 74328

African (AFR) AF: 0.713 AC: 29521 AN: 41430

American (AMR) AF: 0.841 AC: 12855 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2458 AN: 3470

East Asian (EAS) AF: 0.732 AC: 3778 AN: 5162

South Asian (SAS) AF: 0.769 AC: 3704 AN: 4816

European-Finnish (FIN) AF: 0.888 AC: 9405 AN: 10588

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56200 AN: 67954

Other (OTH) AF: 0.768 AC: 1620 AN: 2110

Alfa AF: 0.808 Hom.: 155612

Bravo AF: 0.787

Asia WGS AF: 0.745 AC: 2592 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.65
PhyloP100		-0.55
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: rs9288125; hg19: chr2-153523111;