rs10967942

Positions:

• chr9-2754177-G-A
• chr9-2754177-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000490444.2(PUM3):​c.*126+28579C>T variant causes a intron, NMD transcript 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, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PUM3	ENST00000490444.2	c.*126+28579C>T		intron_variant, NMD_transcript_variant		5		ENSP00000474467

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

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.0595

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.0394

Gnomad4 SAS AF: 0.0160

Gnomad4 FIN AF: 0.0544

Gnomad4 NFE AF: 0.0396

Gnomad4 OTH AF: 0.0969

Alfa AF: 0.0305 Hom.: 56

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10967942; hg19: chr9-2754177;