chr7-150330897-A-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001142928.2(LRRC61):c.-145+4887A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000521 in 1,611,752 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 0.00024 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000032 ( 0 hom. )
Consequence
LRRC61
NM_001142928.2 intron
NM_001142928.2 intron
Scores
1
3
15
Clinical Significance
Conservation
PhyloP100: 0.571
Genes affected
LRRC61 (HGNC:21704): (leucine rich repeat containing 61) Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08565894).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC61 | NM_001142928.2 | c.-145+4887A>T | intron_variant | ENST00000359623.9 | NP_001136400.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152092Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000323 AC: 8AN: 247414Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134484
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GnomAD4 exome AF: 0.0000322 AC: 47AN: 1459660Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 725936
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GnomAD4 genome AF: 0.000243 AC: 37AN: 152092Hom.: 0 Cov.: 33 AF XY: 0.000215 AC XY: 16AN XY: 74308
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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 04, 2024 | The c.493A>T (p.R165W) alteration is located in exon 1 (coding exon 1) of the ZBED6CL gene. This alteration results from a A to T substitution at nucleotide position 493, causing the arginine (R) at amino acid position 165 to be replaced by a tryptophan (W). 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
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
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