1-152218471-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001009931.3(HRNR):​c.3158G>A​(p.Arg1053Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00493 in 1,612,842 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0038 ( 1 hom., cov: 31)
Exomes 𝑓: 0.0051 ( 21 hom. )

Consequence

HRNR
NM_001009931.3 missense

Scores

1
17

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.264
Variant links:
Genes affected
HRNR (HGNC:20846): (hornerin) Predicted to enable calcium ion binding activity and transition metal ion binding activity. Involved in cell envelope organization and establishment of skin barrier. Located in cornified envelope; keratohyalin granule; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
CCDST (HGNC:55988): (cervical cancer associated DHX9 suppressive transcript)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.005783081).
BP6
Variant 1-152218471-C-T is Benign according to our data. Variant chr1-152218471-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2639206.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 21 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HRNRNM_001009931.3 linkc.3158G>A p.Arg1053Gln missense_variant Exon 3 of 3 ENST00000368801.4 NP_001009931.1 Q86YZ3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HRNRENST00000368801.4 linkc.3158G>A p.Arg1053Gln missense_variant Exon 3 of 3 1 NM_001009931.3 ENSP00000357791.3 Q86YZ3

Frequencies

GnomAD3 genomes
AF:
0.00376
AC:
568
AN:
150976
Hom.:
1
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00105
Gnomad AMI
AF:
0.00329
Gnomad AMR
AF:
0.00704
Gnomad ASJ
AF:
0.000289
Gnomad EAS
AF:
0.000199
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00360
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00528
Gnomad OTH
AF:
0.00822
GnomAD3 exomes
AF:
0.00302
AC:
760
AN:
251414
Hom.:
4
AF XY:
0.00302
AC XY:
410
AN XY:
135900
show subpopulations
Gnomad AFR exome
AF:
0.000800
Gnomad AMR exome
AF:
0.00341
Gnomad ASJ exome
AF:
0.0000992
Gnomad EAS exome
AF:
0.000163
Gnomad SAS exome
AF:
0.000196
Gnomad FIN exome
AF:
0.00407
Gnomad NFE exome
AF:
0.00453
Gnomad OTH exome
AF:
0.00261
GnomAD4 exome
AF:
0.00506
AC:
7391
AN:
1461748
Hom.:
21
Cov.:
122
AF XY:
0.00485
AC XY:
3524
AN XY:
727176
show subpopulations
Gnomad4 AFR exome
AF:
0.000597
Gnomad4 AMR exome
AF:
0.00369
Gnomad4 ASJ exome
AF:
0.000191
Gnomad4 EAS exome
AF:
0.0000756
Gnomad4 SAS exome
AF:
0.000186
Gnomad4 FIN exome
AF:
0.00341
Gnomad4 NFE exome
AF:
0.00604
Gnomad4 OTH exome
AF:
0.00464
GnomAD4 genome
AF:
0.00376
AC:
568
AN:
151094
Hom.:
1
Cov.:
31
AF XY:
0.00370
AC XY:
273
AN XY:
73814
show subpopulations
Gnomad4 AFR
AF:
0.00105
Gnomad4 AMR
AF:
0.00703
Gnomad4 ASJ
AF:
0.000289
Gnomad4 EAS
AF:
0.000200
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00360
Gnomad4 NFE
AF:
0.00528
Gnomad4 OTH
AF:
0.00813
Alfa
AF:
0.00315
Hom.:
0
Bravo
AF:
0.00370
ESP6500AA
AF:
0.00113
AC:
5
ESP6500EA
AF:
0.00617
AC:
53
ExAC
AF:
0.00256
AC:
311
EpiCase
AF:
0.00442
EpiControl
AF:
0.00439

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jan 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

HRNR: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.078
BayesDel_addAF
Benign
-0.71
T
BayesDel_noAF
Benign
-0.80
CADD
Benign
5.1
DANN
Benign
0.64
DEOGEN2
Benign
0.014
T
Eigen
Benign
-2.0
Eigen_PC
Benign
-2.0
FATHMM_MKL
Benign
0.00011
N
LIST_S2
Benign
0.30
T
MetaRNN
Benign
0.0058
T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
-0.76
N
PrimateAI
Uncertain
0.58
T
PROVEAN
Benign
0.14
N
REVEL
Benign
0.012
Sift
Benign
0.16
T
Sift4G
Benign
0.65
T
Polyphen
0.0010
B
Vest4
0.047
MVP
0.19
ClinPred
0.0012
T
GERP RS
-2.6
Varity_R
0.024
gMVP
0.0097

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: rs142424978; hg19: chr1-152190947; API