chr14-20891137-G-A

Variant names:

• chr14-20891137-G-A
• rs2284954
• ENST00000717679.1:n.259-15394C>T

Variant summary

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

The ENST00000717679.1(ENSG00000259130):​n.259-15394C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 150,674 control chromosomes in the GnomAD database, including 31,183 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 0.61 (31183 hom., cov: 31)
• Consequence: ENSG00000259130 ENST00000717679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• Publications: 4 publications found

Genes affected

ENSG00000259130 (HGNC:):

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507513	XR_110261.4	n.723-15394C>T		intron_variant	Intron 1 of 3
RNASE3	NM_002935.3	c.-320G>A		upstream_gene_variant		ENST00000304639.4	NP_002926.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNASE3	ENST00000304639.4	c.-320G>A		upstream_gene_variant		1	NM_002935.3	ENSP00000302324.3

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91245 AN: 150556 Hom.: 31166 Cov.: 31

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.606 AC: 91278 AN: 150674 Hom.: 31183 Cov.: 31 AF XY: 0.609 AC XY: 44860 AN XY: 73608

African (AFR) AF: 0.278 AC: 11191 AN: 40194

American (AMR) AF: 0.750 AC: 11419 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2456 AN: 3466

East Asian (EAS) AF: 0.622 AC: 3212 AN: 5166

South Asian (SAS) AF: 0.689 AC: 3303 AN: 4792

European-Finnish (FIN) AF: 0.766 AC: 8083 AN: 10550

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49477 AN: 67980

Other (OTH) AF: 0.635 AC: 1333 AN: 2098

Alfa AF: 0.673 Hom.: 4642

Bravo AF: 0.586

Asia WGS AF: 0.639 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.58
PhyloP100		-0.20
PromoterAI		0.035	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2284954; hg19: chr14-21359296;