rs7970954
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001352232.2(LMNTD1):c.-283+6321A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,992 control chromosomes in the GnomAD database, including 19,986 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 0.48 ( 19986 hom., cov: 31)
Consequence
LMNTD1
NM_001352232.2 intron
NM_001352232.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0270
Genes affected
LMNTD1 (HGNC:26683): (lamin tail domain containing 1) Predicted to act upstream of or within cell population proliferation. Predicted to be located in nucleus. Predicted to be active in cytoplasm and nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMNTD1 | NM_001145727.3 | c.58+6321A>G | intron_variant | ||||
LMNTD1 | NM_001352232.2 | c.-283+6321A>G | intron_variant | ||||
LMNTD1 | NM_001352233.2 | c.-92+6321A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMNTD1 | ENST00000445693.5 | c.58+6321A>G | intron_variant | 2 | A2 | ||||
LMNTD1 | ENST00000540106.5 | c.-50+6321A>G | intron_variant | 4 | |||||
LMNTD1 | ENST00000542224.1 | c.-223+6321A>G | intron_variant | 5 | |||||
LMNTD1 | ENST00000545543.1 | c.-83+6321A>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.480 AC: 72964AN: 151874Hom.: 19993 Cov.: 31
GnomAD3 genomes
?
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72964
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.480 AC: 72976AN: 151992Hom.: 19986 Cov.: 31 AF XY: 0.478 AC XY: 35480AN XY: 74300
GnomAD4 genome
?
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35480
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1418
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at