chr14-77715845-T-A
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_031210.6(SLIRP):c.230T>A(p.Leu77Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000235 in 1,613,948 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00024 ( 0 hom. )
Consequence
SLIRP
NM_031210.6 missense
NM_031210.6 missense
Scores
8
6
Clinical Significance
Conservation
PhyloP100: 6.35
Genes affected
SLIRP (HGNC:20495): (SRA stem-loop interacting RNA binding protein) Steroid receptor RNA activator (SRA, or SRA1; MIM 603819) is a complex RNA molecule containing multiple stable stem-loop structures that functions in coactivation of nuclear receptors. SLIRP interacts with stem-loop structure-7 of SRA (STR7) and modulates nuclear receptor transactivation (Hatchell et al., 2006 [PubMed 16762838]).[supplied by OMIM, Mar 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLIRP | NM_031210.6 | c.230T>A | p.Leu77Gln | missense_variant | 3/4 | ENST00000557342.6 | |
SLIRP | NM_001267863.1 | c.230T>A | p.Leu77Gln | missense_variant | 3/4 | ||
SLIRP | NM_001267864.1 | c.230T>A | p.Leu77Gln | missense_variant | 3/4 | ||
SLIRP | NR_052025.2 | n.350T>A | non_coding_transcript_exon_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLIRP | ENST00000557342.6 | c.230T>A | p.Leu77Gln | missense_variant | 3/4 | 1 | NM_031210.6 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152176Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
30
AN:
152176
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:
GnomAD3 exomes AF: 0.000196 AC: 49AN: 250452Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135780
GnomAD3 exomes
AF:
AC:
49
AN:
250452
Hom.:
AF XY:
AC XY:
27
AN XY:
135780
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000239 AC: 349AN: 1461772Hom.: 0 Cov.: 30 AF XY: 0.000245 AC XY: 178AN XY: 727182
GnomAD4 exome
AF:
AC:
349
AN:
1461772
Hom.:
Cov.:
30
AF XY:
AC XY:
178
AN XY:
727182
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000197 AC: 30AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74346
GnomAD4 genome
AF:
AC:
30
AN:
152176
Hom.:
Cov.:
32
AF XY:
AC XY:
14
AN XY:
74346
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:
ESP6500AA
AF:
AC:
0
ESP6500EA
AF:
AC:
2
ExAC
AF:
AC:
28
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.230T>A (p.L77Q) alteration is located in exon 3 (coding exon 3) of the SLIRP gene. This alteration results from a T to A substitution at nucleotide position 230, causing the leucine (L) at amino acid position 77 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D;D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
Sift4G
Uncertain
D;D;D;D;D
Polyphen
1.0
.;D;.;.;.
Vest4
MVP
MPC
0.56
ClinPred
T
GERP RS
Varity_R
gMVP
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