rs9459805

Positions:

• chr6-166922663-A-G

Variant summary

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

The NM_003730.6(RNASET2):​c.*6925T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,166 control chromosomes in the GnomAD database, including 8,253 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 0.27 (8253 hom., cov: 33)
• Consequence: RNASET2 NM_003730.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777

Genes affected

RNASET2 (HGNC:21686): (ribonuclease T2) This ribonuclease gene is a novel member of the Rh/T2/S-glycoprotein class of extracellular ribonucleases. It is a single copy gene that maps to 6q27, a region associated with human malignancies and chromosomal rearrangement. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNASET2	NM_003730.6	c.*6925T>C		3_prime_UTR_variant	9/9	ENST00000508775.6	NP_003721.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNASET2	ENST00000508775.6	c.*6925T>C		3_prime_UTR_variant	9/9	1	NM_003730.6	ENSP00000426455	P1

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41045 AN: 152048 Hom.: 8215 Cov.: 33

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0983

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.270 AC: 41139 AN: 152166 Hom.: 8253 Cov.: 33 AF XY: 0.266 AC XY: 19769 AN XY: 74386

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.0980

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.250

Alfa AF: 0.225 Hom.: 1550

Bravo AF: 0.286

Asia WGS AF: 0.217 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9459805; hg19: chr6-167336151;