rs1377347
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000313860.12(LIMCH1):c.96+9649T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 151,914 control chromosomes in the GnomAD database, including 14,831 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 0.42 ( 14831 hom., cov: 32)
Consequence
LIMCH1
ENST00000313860.12 intron
ENST00000313860.12 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.429
Genes affected
LIMCH1 (HGNC:29191): (LIM and calponin homology domains 1) Enables myosin II head/neck binding activity. Involved in several processes, including cytoplasmic actin-based contraction involved in cell motility; positive regulation of stress fiber assembly; and regulation of focal adhesion assembly. Located in stress fiber. Colocalizes with myosin II complex. [provided by Alliance of Genome Resources, Apr 2022]
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 (BayesDel_noAF=-0.6).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIMCH1 | NM_001112717.4 | c.96+9649T>G | intron_variant | ||||
LIMCH1 | NM_001112718.4 | c.96+9649T>G | intron_variant | ||||
LIMCH1 | NM_001289122.3 | c.96+9649T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIMCH1 | ENST00000313860.12 | c.96+9649T>G | intron_variant | 1 | P3 | ||||
LIMCH1 | ENST00000508501.5 | c.96+9649T>G | intron_variant | 1 | A1 | ||||
LIMCH1 | ENST00000509638.5 | c.-311+9649T>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.418 AC: 63449AN: 151796Hom.: 14810 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
63449
AN:
151796
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.418 AC: 63520AN: 151914Hom.: 14831 Cov.: 32 AF XY: 0.419 AC XY: 31121AN XY: 74228
GnomAD4 genome
?
AF:
AC:
63520
AN:
151914
Hom.:
Cov.:
32
AF XY:
AC XY:
31121
AN XY:
74228
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:
Asia WGS
AF:
AC:
1458
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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