6-166957622-T-C

Variant names:

• chr6-166957622-T-C
• rs2149085
• ENST00000870280.1:c.-245A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000870280.1(RNASET2):​c.-245A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,226 control chromosomes in the GnomAD database, including 26,319 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 0.58 (26319 hom., cov: 34)
• Consequence: RNASET2 ENST00000870280.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72
• Publications: 36 publications found

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]

RNASET2 Gene-Disease associations (from GenCC):

• cystic leukoencephalopathy without megalencephaly

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics, Orphanet, Illumina

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000870280.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNASET2	ENST00000870280.1		c.-245A>G		upstream_gene	N/A	ENSP00000540339.1
	RNASET2	ENST00000870281.1		c.-404A>G		upstream_gene	N/A	ENSP00000540340.1

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87622 AN: 152108 Hom.: 26266 Cov.: 34

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.576 AC: 87733 AN: 152226 Hom.: 26319 Cov.: 34 AF XY: 0.582 AC XY: 43288 AN XY: 74432

African (AFR) AF: 0.737 AC: 30592 AN: 41522

American (AMR) AF: 0.611 AC: 9355 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1827 AN: 3470

East Asian (EAS) AF: 0.621 AC: 3225 AN: 5192

South Asian (SAS) AF: 0.696 AC: 3356 AN: 4824

European-Finnish (FIN) AF: 0.533 AC: 5650 AN: 10594

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31818 AN: 68010

Other (OTH) AF: 0.588 AC: 1242 AN: 2114

Alfa AF: 0.594 Hom.: 11789

Bravo AF: 0.591

Asia WGS AF: 0.667 AC: 2318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.38
PhyloP100		-2.7
PromoterAI		-0.022	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2149085; hg19: chr6-167371110;