rs8019343

Variant names:

• chr14-20892263-A-T
• rs8019343
• NM_002935.3:c.*94A>T

Variant summary

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

The NM_002935.3(RNASE3):​c.*94A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00841 in 1,508,100 control chromosomes in the GnomAD database, including 1,271 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 0.040 (702 hom., cov: 31)
  • Exomes 𝑓: 0.0049 (569 hom.)
• Consequence: RNASE3 NM_002935.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566
• Publications: 6 publications found

Genes affected

RNASE3 (HGNC:10046): (ribonuclease A family member 3) The protein encoded by this gene belongs to the pancreatic ribonuclease family, a subset of the ribonuclease A superfamily. The protein exhibits antimicrobial activity against pathogenic bacteria [provided by RefSeq, Oct 2014]

ENSG00000259130 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002935.3. 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
	RNASE3	NM_002935.3	MANE Select	c.*94A>T		3_prime_UTR	Exon 2 of 2	NP_002926.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNASE3	ENST00000304639.4	TSL:1 MANE Select	c.*94A>T		3_prime_UTR	Exon 2 of 2	ENSP00000302324.3	P12724
	ENSG00000259130	ENST00000717679.1		n.259-16520T>A		intron	N/A
	ENSG00000259130	ENST00000717680.1		n.347-16520T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0402 AC: 6069 AN: 150938 Hom.: 695 Cov.: 31

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0197

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.000471

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00141

Gnomad OTH AF: 0.0360

GnomAD4 exome AF: 0.00486 AC: 6595 AN: 1357044 Hom.: 569 Cov.: 24 AF XY: 0.00445 AC XY: 2980 AN XY: 669828

African (AFR) AF: 0.142 AC: 4134 AN: 29064

American (AMR) AF: 0.0102 AC: 330 AN: 32382

Ashkenazi Jewish (ASJ) AF: 0.00687 AC: 141 AN: 20524

East Asian (EAS) AF: 0.00 AC: 0 AN: 39104

South Asian (SAS) AF: 0.000576 AC: 41 AN: 71124

European-Finnish (FIN) AF: 0.000518 AC: 26 AN: 50148

Middle Eastern (MID) AF: 0.0147 AC: 78 AN: 5300

European-Non Finnish (NFE) AF: 0.00118 AC: 1244 AN: 1053332

Other (OTH) AF: 0.0107 AC: 601 AN: 56066

GnomAD4 genome AF: 0.0403 AC: 6095 AN: 151056 Hom.: 702 Cov.: 31 AF XY: 0.0380 AC XY: 2810 AN XY: 73862

African (AFR) AF: 0.138 AC: 5587 AN: 40410

American (AMR) AF: 0.0197 AC: 300 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.00720 AC: 25 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4816

European-Finnish (FIN) AF: 0.000471 AC: 5 AN: 10622

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00141 AC: 96 AN: 68004

Other (OTH) AF: 0.0356 AC: 75 AN: 2104

Alfa AF: 0.0368 Hom.: 58

Bravo AF: 0.0470

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.52
DANN	Benign	0.55
PhyloP100		-0.57
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8019343; hg19: chr14-21360422;