chr9-2754177-G-A

Variant names:

• chr9-2754177-G-A
• rs10967942
• ENST00000490444.2:n.*126+28579C>T

Variant summary

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

The ENST00000490444.2(PUM3):​n.*126+28579C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,016 control chromosomes in the GnomAD database, including 3,314 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 0.14 (3314 hom., cov: 32)
• Consequence: PUM3 ENST00000490444.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901
• Publications: 0 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PUM3	ENST00000490444.2	n.*126+28579C>T		intron_variant	Intron 3 of 3	5		ENSP00000474467.1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20888 AN: 151898 Hom.: 3298 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.0393

Gnomad SAS AF: 0.0164

Gnomad FIN AF: 0.0544

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0396

Gnomad OTH AF: 0.0979

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

GnomAD4 genome AF: 0.138 AC: 20940 AN: 152016 Hom.: 3314 Cov.: 32 AF XY: 0.134 AC XY: 9948 AN XY: 74306

African (AFR) AF: 0.390 AC: 16175 AN: 41442

American (AMR) AF: 0.0595 AC: 909 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3472

East Asian (EAS) AF: 0.0394 AC: 204 AN: 5176

South Asian (SAS) AF: 0.0160 AC: 77 AN: 4816

European-Finnish (FIN) AF: 0.0544 AC: 575 AN: 10570

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0396 AC: 2688 AN: 67950

Other (OTH) AF: 0.0969 AC: 204 AN: 2106

Alfa AF: 0.0659 Hom.: 1202

Bravo AF: 0.150

Asia WGS AF: 0.0410 AC: 142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.35
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs10967942; hg19: chr9-2754177;