rs10812641

Variant names:

• chr9-2777384-T-A
• rs10812641
• ENST00000490444.2:n.*126+5372A>T

Your query was ambiguous. Multiple possible variants found:

• chr9-2777384-T-A
• chr9-2777384-T-C

Variant summary

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

The ENST00000490444.2(PUM3):​n.*126+5372A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,818 control chromosomes in the GnomAD database, including 13,052 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 0.40 (13052 hom., cov: 33)
• Consequence: PUM3 ENST00000490444.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

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=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.473 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+5372A>T		intron_variant	Intron 3 of 3	5		ENSP00000474467.1

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60096 AN: 151698 Hom.: 13050 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.396 AC: 60100 AN: 151818 Hom.: 13052 Cov.: 33 AF XY: 0.398 AC XY: 29503 AN XY: 74192

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.407

Alfa AF: 0.320 Hom.: 945

Bravo AF: 0.391

Asia WGS AF: 0.387 AC: 1343 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.9
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10812641; hg19: chr9-2777384;