chr7-104328851-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_199000.3(LHFPL3):c.72G>A(p.Leu24=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00152 in 1,614,178 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0082 ( 16 hom., cov: 33)
Exomes 𝑓: 0.00083 ( 17 hom. )
Consequence
LHFPL3
NM_199000.3 synonymous
NM_199000.3 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 0.331
Genes affected
LHFPL3 (HGNC:6589): (LHFPL tetraspan subfamily member 3) This gene is a member of the lipoma HMGIC fusion partner (LHFP) gene family, which is a subset of the superfamily of tetraspan transmembrane protein encoding genes. Mutations in one LHFP-like gene result in deafness in humans and mice, and a second LHFP-like gene is fused to a high-mobility group gene in a translocation-associated lipoma. A partial gene fragment named LHFPL4 corresponds to a portion of the first exon of this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
?
Variant 7-104328851-G-A is Benign according to our data. Variant chr7-104328851-G-A is described in ClinVar as [Benign]. Clinvar id is 786772.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.331 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00816 (1243/152342) while in subpopulation AFR AF= 0.0289 (1200/41592). AF 95% confidence interval is 0.0275. There are 16 homozygotes in gnomad4. There are 598 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 16 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LHFPL3 | NM_199000.3 | c.72G>A | p.Leu24= | synonymous_variant | 1/3 | ENST00000424859.7 | |
LHFPL3 | NM_001386065.1 | c.72G>A | p.Leu24= | synonymous_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LHFPL3 | ENST00000424859.7 | c.72G>A | p.Leu24= | synonymous_variant | 1/3 | 1 | NM_199000.3 | P1 | |
LHFPL3 | ENST00000401970.3 | c.72G>A | p.Leu24= | synonymous_variant | 1/4 | 1 | |||
LHFPL3 | ENST00000683240.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00819 AC: 1246AN: 152224Hom.: 16 Cov.: 33
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GnomAD3 exomes AF: 0.00202 AC: 503AN: 249174Hom.: 2 AF XY: 0.00139 AC XY: 188AN XY: 135210
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GnomAD4 exome AF: 0.000829 AC: 1212AN: 1461836Hom.: 17 Cov.: 34 AF XY: 0.000667 AC XY: 485AN XY: 727218
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GnomAD4 genome ? AF: 0.00816 AC: 1243AN: 152342Hom.: 16 Cov.: 33 AF XY: 0.00803 AC XY: 598AN XY: 74484
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at