dbSNP rs11575981: ENSG00000259130:n.259-15551G>A (chr14-20891294-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.371

Publications

1 publications found

Variant links:

Genes affected

ENSG00000259130 (HGNC:):

ENSG00000259130 links:

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]

RNASE3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507513	XR_110261.4 link	n.723-15551G>A		intron_variant	Intron 1 of 3
RNASE3	NM_002935.3 link	c.-163C>T		upstream_gene_variant		ENST00000304639.4	NP_002926.2	P12724

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNASE3	ENST00000304639.4 link	c.-163C>T		upstream_gene_variant		1	NM_002935.3	ENSP00000302324.3		P12724

Frequencies

GnomAD3 genomes

AF:

0.00706

AC:

1066

AN:

151054

Hom.:

Cov.:

show subpopulations

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.:

AF XY:

0.00623

AC XY:

206

AN XY:

33070

show subpopulations

African (AFR)

AF:

0.00225

AC:

AN:

1332

American (AMR)

AF:

0.00381

AC:

AN:

4196

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1816

East Asian (EAS)

AF:

0.0724

AC:

280

AN:

3868

South Asian (SAS)

AF:

0.00222

AC:

AN:

5862

European-Finnish (FIN)

AF:

0.0301

AC:

AN:

2528

Middle Eastern (MID)

AF:

0.00

AC:

AN:

274

European-Non Finnish (NFE)

AF:

0.000746

AC:

AN:

41548

Other (OTH)

AF:

0.00462

AC:

AN:

3900

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

104

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00705

AC:

1065

AN:

151170

Hom.:

Cov.:

AF XY:

0.00917

AC XY:

678

AN XY:

73940

show subpopulations

African (AFR)

AF:

0.00123

AC:

AN:

40528

American (AMR)

AF:

0.00144

AC:

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.106

AC:

548

AN:

5174

South Asian (SAS)

AF:

0.00395

AC:

AN:

4814

European-Finnish (FIN)

AF:

0.0336

AC:

357

AN:

10612

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000867

AC:

AN:

68024

Other (OTH)

AF:

0.00475

AC:

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

107

160

214

267

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00237

Hom.:

Bravo

AF:

0.00488

Asia WGS

AF:

0.0530

AC:

182

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

9.1

(source)

DANN

Benign

0.69

PhyloP100

0.37

PromoterAI

-0.24

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over