rs7857841

Variant names:

• chr9-2756756-A-C
• rs7857841
• ENST00000490444.2:n.*126+26000T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-2756756-A-C
• chr9-2756756-A-G
• chr9-2756756-A-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+26000T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.884 in 152,154 control chromosomes in the GnomAD database, including 59,650 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 0.88 (59650 hom., cov: 31)
• Consequence: PUM3 ENST00000490444.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756
• Publications: 6 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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+26000T>G		intron_variant	Intron 3 of 3	5		ENSP00000474467.1

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134438 AN: 152036 Hom.: 59598 Cov.: 31

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.885

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

GnomAD4 genome AF: 0.884 AC: 134550 AN: 152154 Hom.: 59650 Cov.: 31 AF XY: 0.886 AC XY: 65897 AN XY: 74386

African (AFR) AF: 0.825 AC: 34220 AN: 41476

American (AMR) AF: 0.914 AC: 13981 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2989 AN: 3472

East Asian (EAS) AF: 0.973 AC: 5042 AN: 5184

South Asian (SAS) AF: 0.918 AC: 4427 AN: 4820

European-Finnish (FIN) AF: 0.884 AC: 9364 AN: 10588

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.905 AC: 61551 AN: 68006

Other (OTH) AF: 0.884 AC: 1866 AN: 2110

Alfa AF: 0.895 Hom.: 83947

Bravo AF: 0.883

Asia WGS AF: 0.918 AC: 3190 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.72
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs7857841; hg19: chr9-2756756;