9-2756638-C-T

Variant names:

• chr9-2756638-C-T
• rs10967953
• ENST00000490444.2:n.*126+26118G>A

Variant summary

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

The ENST00000490444.2(PUM3):​n.*126+26118G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,042 control chromosomes in the GnomAD database, including 46,159 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 0.78 (46159 hom., cov: 31)
• Consequence: PUM3 ENST00000490444.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 4 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000490444.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PUM3	ENST00000490444.2	TSL:5	n.*126+26118G>A		intron	N/A	ENSP00000474467.1

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118040 AN: 151924 Hom.: 46139 Cov.: 31

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.777 AC: 118107 AN: 152042 Hom.: 46159 Cov.: 31 AF XY: 0.779 AC XY: 57871 AN XY: 74302

African (AFR) AF: 0.676 AC: 28004 AN: 41440

American (AMR) AF: 0.793 AC: 12118 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2603 AN: 3470

East Asian (EAS) AF: 0.864 AC: 4462 AN: 5164

South Asian (SAS) AF: 0.865 AC: 4165 AN: 4814

European-Finnish (FIN) AF: 0.778 AC: 8212 AN: 10554

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.821 AC: 55845 AN: 67994

Other (OTH) AF: 0.793 AC: 1677 AN: 2114

Alfa AF: 0.798 Hom.: 22088

Bravo AF: 0.771

Asia WGS AF: 0.823 AC: 2861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.34
DANN	Benign	0.29
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs10967953; hg19: chr9-2756638;