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GeneBe

14-20781791-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_005615.5(RNASE6):c.92C>G(p.Ala31Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000789 in 152166 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000079 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000076 ( 0 hom. )

Consequence

RNASE6
NM_005615.5 missense

Scores

1
7
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.03

Links

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RNASE6NM_005615.5 linkuse as main transcriptc.92C>G p.Ala31Gly missense_variant 2/2 ENST00000304677.3
LOC107984671XR_001750624.2 linkuse as main transcriptn.626+18113G>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RNASE6ENST00000304677.3 linkuse as main transcriptc.92C>G p.Ala31Gly missense_variant 2/21 NM_005615.5 P1

Frequencies

GnomAD3 genomes
AF:
0.0000789
AC:
12
AN:
152166
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000132
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000756
AC:
19
AN:
251466
Hom.:
0
AF XY:
0.0000736
AC XY:
10
AN XY:
135904
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.0000867
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000462
Gnomad NFE exome
AF:
0.000123
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000670
AC:
98
AN:
1461888
Hom.:
0
AF XY:
0.0000633
AC XY:
46
AN XY:
727248
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000894
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.0000719
Gnomad4 OTH exome
AF:
0.000215
Alfa
AF:
0.0000279
Hom.:
0
Bravo
AF:
0.0000378
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1
ExAC
AF:
0.000107
AC:
13
EpiCase
AF:
0.000109
EpiControl
AF:
0.0000593

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMay 11, 2022The c.92C>G (p.A31G) alteration is located in exon 2 (coding exon 1) of the RNASE6 gene. This alteration results from a C to G substitution at nucleotide position 92, causing the alanine (A) at amino acid position 31 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.21
BayesDel_addAF
Benign
-0.16
T
BayesDel_noAF
Benign
-0.23
Cadd
Benign
22
Dann
Uncertain
1.0
DEOGEN2
Benign
0.21
T
Eigen
Uncertain
0.22
Eigen_PC
Benign
-0.015
FATHMM_MKL
Benign
0.13
N
LIST_S2
Benign
0.66
T
M_CAP
Benign
0.070
D
MetaRNN
Uncertain
0.73
D
MetaSVM
Uncertain
-0.18
T
MutationAssessor
Pathogenic
3.9
H
MutationTaster
Benign
1.0
N
PrimateAI
Benign
0.41
T
PROVEAN
Uncertain
-2.9
D
REVEL
Uncertain
0.38
Sift
Benign
0.038
D
Sift4G
Uncertain
0.016
D
Polyphen
1.0
D
Vest4
0.31
MutPred
0.77
Gain of methylation at K26 (P = 0.0882);
MVP
0.95
MPC
0.46
ClinPred
0.84
D
GERP RS
4.2
Varity_R
0.82
gMVP
0.62

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200834282; hg19: chr14-21249950; API