rs4705403
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014983.3(HMGXB3):c.-252G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 154,684 control chromosomes in the GnomAD database, including 1,341 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 0.12 ( 1297 hom., cov: 32)
Exomes 𝑓: 0.15 ( 44 hom. )
Consequence
HMGXB3
NM_014983.3 5_prime_UTR
NM_014983.3 5_prime_UTR
Scores
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.263
Genes affected
HMGXB3 (HGNC:28982): (HMG-box containing 3) This gene is one of the non-canonical high mobility group (HMG) genes. The encoded protein contains an HMG-box domain found in DNA binding proteins such as transcription factors and chromosomal proteins. [provided by RefSeq, Aug 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0015045702).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HMGXB3 | NM_014983.3 | c.-252G>A | 5_prime_UTR_variant | 1/20 | ENST00000502717.6 | ||
HMGXB3 | NM_001366501.2 | c.-252G>A | 5_prime_UTR_variant | 1/19 | |||
HMGXB3 | XM_047416963.1 | c.-252G>A | 5_prime_UTR_variant | 1/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HMGXB3 | ENST00000502717.6 | c.-252G>A | 5_prime_UTR_variant | 1/20 | 1 | NM_014983.3 | P2 | ||
HMGXB3 | ENST00000613459.4 | c.487G>A | p.Glu163Lys | missense_variant | 2/21 | 5 | A2 | ||
HMGXB3 | ENST00000503427.5 | c.-252G>A | 5_prime_UTR_variant | 1/21 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.119 AC: 18033AN: 151948Hom.: 1298 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
18033
AN:
151948
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.151 AC: 396AN: 2618Hom.: 44 Cov.: 0 AF XY: 0.133 AC XY: 179AN XY: 1344
GnomAD4 exome
AF:
AC:
396
AN:
2618
Hom.:
Cov.:
0
AF XY:
AC XY:
179
AN XY:
1344
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.119 AC: 18035AN: 152066Hom.: 1297 Cov.: 32 AF XY: 0.119 AC XY: 8865AN XY: 74326
GnomAD4 genome
?
AF:
AC:
18035
AN:
152066
Hom.:
Cov.:
32
AF XY:
AC XY:
8865
AN XY:
74326
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
420
ALSPAC
AF:
AC:
376
Asia WGS
AF:
AC:
287
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MutationTaster
Benign
P;P;P
Sift4G
Benign
T
Vest4
MVP
GERP RS
Varity_R
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at