rs3798305

chr6-166949985-C-T

Variant summary

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

The NM_003730.6(RNASET2):c.148-1360G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0415 in 152,356 control chromosomes in the GnomAD database, including 246 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 0.042 (246 hom., cov: 33)
• Consequence: RNASET2 NM_003730.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNASET2	NM_003730.6	c.148-1360G>A		intron_variant		ENST00000508775.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNASET2	ENST00000508775.6	c.148-1360G>A		intron_variant		1	NM_003730.6	P1

Frequencies

GnomAD3 genomes AF: 0.0414 AC: 6310 AN: 152238 Hom.: 244 Cov.: 33

Gnomad AFR AF: 0.0966

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0257

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.0875

Gnomad SAS AF: 0.0374

Gnomad FIN AF: 0.00489

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0157

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0415 AC: 6330 AN: 152356 Hom.: 246 Cov.: 33 AF XY: 0.0417 AC XY: 3107 AN XY: 74506

Gnomad4 AFR AF: 0.0969

Gnomad4 AMR AF: 0.0256

Gnomad4 ASJ AF: 0.0202

Gnomad4 EAS AF: 0.0875

Gnomad4 SAS AF: 0.0372

Gnomad4 FIN AF: 0.00489

Gnomad4 NFE AF: 0.0156

Gnomad4 OTH AF: 0.0369

Alfa AF: 0.0216 Hom.: 64

Bravo AF: 0.0460

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.80
Dann	Benign	0.19

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: rs3798305; hg19: chr6-167363473;