rs11575981

Variant names:

• chr14-20891294-C-T
• rs11575981
• ENST00000717679.1:n.259-15551G>A

Variant summary

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

The ENST00000717679.1(ENSG00000259130):​n.259-15551G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00694 in 216,494 control chromosomes in the GnomAD database, including 44 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 0.0070 (28 hom., cov: 31)
  • Exomes 𝑓: 0.0067 (16 hom.)
• Consequence: ENSG00000259130 ENST00000717679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0986 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717679.1. 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
	RNASE3	NM_002935.3	MANE Select	c.-163C>T		upstream_gene	N/A	NP_002926.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259130	ENST00000717679.1		n.259-15551G>A		intron	N/A
	ENSG00000259130	ENST00000717680.1		n.347-15551G>A		intron	N/A
	ENSG00000259130	ENST00000717681.1		n.285-15551G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00706 AC: 1066 AN: 151054 Hom.: 28 Cov.: 31

Gnomad AFR AF: 0.00124

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00145

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.00394

Gnomad FIN AF: 0.0336

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000867

Gnomad OTH AF: 0.00432

GnomAD4 exome AF: 0.00669 AC: 437 AN: 65324 Hom.: 16 AF XY: 0.00623 AC XY: 206 AN XY: 33070

African (AFR) AF: 0.00225 AC: 3 AN: 1332

American (AMR) AF: 0.00381 AC: 16 AN: 4196

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1816

East Asian (EAS) AF: 0.0724 AC: 280 AN: 3868

South Asian (SAS) AF: 0.00222 AC: 13 AN: 5862

European-Finnish (FIN) AF: 0.0301 AC: 76 AN: 2528

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 274

European-Non Finnish (NFE) AF: 0.000746 AC: 31 AN: 41548

Other (OTH) AF: 0.00462 AC: 18 AN: 3900

GnomAD4 genome AF: 0.00705 AC: 1065 AN: 151170 Hom.: 28 Cov.: 31 AF XY: 0.00917 AC XY: 678 AN XY: 73940

African (AFR) AF: 0.00123 AC: 50 AN: 40528

American (AMR) AF: 0.00144 AC: 22 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.106 AC: 548 AN: 5174

South Asian (SAS) AF: 0.00395 AC: 19 AN: 4814

European-Finnish (FIN) AF: 0.0336 AC: 357 AN: 10612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000867 AC: 59 AN: 68024

Other (OTH) AF: 0.00475 AC: 10 AN: 2104

Alfa AF: 0.00237 Hom.: 0

Bravo AF: 0.00488

Asia WGS AF: 0.0530 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.1
DANN	Benign	0.69
PhyloP100		0.37
PromoterAI		-0.24	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11575981; hg19: chr14-21359453;