rs8019343

Positions:

• chr14-20892263-A-T

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC100507513 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNASE3	NM_002935.3	c.*94A>T		3_prime_UTR_variant	2/2	ENST00000304639.4	NP_002926.2
LOC100507513	XR_110261.4	n.723-16520T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNASE3	ENST00000304639.4	c.*94A>T		3_prime_UTR_variant	2/2	1	NM_002935.3	ENSP00000302324.3

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

Gnomad4 AFR exome AF: 0.142

Gnomad4 AMR exome AF: 0.0102

Gnomad4 ASJ exome AF: 0.00687

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000576

Gnomad4 FIN exome AF: 0.000518

Gnomad4 NFE exome AF: 0.00118

Gnomad4 OTH exome AF: 0.0107

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

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.0197

Gnomad4 ASJ AF: 0.00720

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000208

Gnomad4 FIN AF: 0.000471

Gnomad4 NFE AF: 0.00141

Gnomad4 OTH AF: 0.0356

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.52
DANN	Benign	0.55

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: rs8019343; hg19: chr14-21360422;