9-2742771-T-C

Variant names:

• chr9-2742771-T-C
• rs2034764
• ENST00000490444.2:n.*127-22239A>G

Variant summary

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

The ENST00000768783.1(ENSG00000286670):​n.113+3527A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,084 control chromosomes in the GnomAD database, including 24,224 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 0.55 (24224 hom., cov: 32)
• Consequence: ENSG00000286670 ENST00000768783.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 12 publications found

Genes affected

PUM3 (HGNC:29676): (pumilio RNA binding family member 3) Enables RNA binding activity. Involved in regulation of protein ADP-ribosylation. Located in chromosome; endoplasmic reticulum; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000286670 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000768783.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PUM3	ENST00000490444.2	TSL:5	n.*127-22239A>G		intron	N/A	ENSP00000474467.1	S4R3K8
	ENSG00000286670	ENST00000768783.1		n.113+3527A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83733 AN: 151966 Hom.: 24162 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.551 AC: 83853 AN: 152084 Hom.: 24224 Cov.: 32 AF XY: 0.551 AC XY: 40958 AN XY: 74346

African (AFR) AF: 0.711 AC: 29471 AN: 41454

American (AMR) AF: 0.602 AC: 9213 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1759 AN: 3470

East Asian (EAS) AF: 0.714 AC: 3692 AN: 5174

South Asian (SAS) AF: 0.382 AC: 1841 AN: 4822

European-Finnish (FIN) AF: 0.498 AC: 5266 AN: 10572

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.456 AC: 30974 AN: 67984

Other (OTH) AF: 0.542 AC: 1144 AN: 2110

Alfa AF: 0.504 Hom.: 46089

Bravo AF: 0.573

Asia WGS AF: 0.582 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.68
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2034764; hg19: chr9-2742771;