chr6-42829414-G-A
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001393499.1(BICRAL):c.1081G>A(p.Val361Met) variant causes a missense change. The variant allele was found at a frequency of 0.000129 in 1,614,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00052 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000088 ( 0 hom. )
Consequence
BICRAL
NM_001393499.1 missense
NM_001393499.1 missense
Scores
4
4
10
Clinical Significance
Conservation
PhyloP100: 6.41
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.06191215).
BS2
High AC in GnomAd4 at 79 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BICRAL | NM_001393499.1 | c.1081G>A | p.Val361Met | missense_variant | 6/13 | ENST00000314073.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BICRAL | ENST00000314073.10 | c.1081G>A | p.Val361Met | missense_variant | 6/13 | 1 | NM_001393499.1 | P1 | |
BICRAL | ENST00000394168.1 | c.1081G>A | p.Val361Met | missense_variant | 5/12 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000519 AC: 79AN: 152200Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000127 AC: 32AN: 251430Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135890
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GnomAD4 exome AF: 0.0000882 AC: 129AN: 1461868Hom.: 0 Cov.: 34 AF XY: 0.0000894 AC XY: 65AN XY: 727240
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GnomAD4 genome AF: 0.000519 AC: 79AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74490
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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 | Oct 06, 2021 | The c.1081G>A (p.V361M) alteration is located in exon 5 (coding exon 4) of the GLTSCR1L gene. This alteration results from a G to A substitution at nucleotide position 1081, causing the valine (V) at amino acid position 361 to be replaced by a methionine (M). 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
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;.;.
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
T
PROVEAN
Benign
.;N;N
REVEL
Benign
Sift
Uncertain
.;D;D
Sift4G
Uncertain
D;D;D
Polyphen
D;D;D
Vest4
MVP
MPC
0.79
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at