rs78015633
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2
The NM_001258419.2(LRRC4C):c.-407+78599A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0089 in 152,270 control chromosomes in the GnomAD database, including 6 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 0.0089 ( 6 hom., cov: 33)
Consequence
LRRC4C
NM_001258419.2 intron
NM_001258419.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.50
Genes affected
LRRC4C (HGNC:29317): (leucine rich repeat containing 4C) NGL1 is a specific binding partner for netrin G1 (NTNG1; MIM 608818), which is a member of the netrin family of axon guidance molecules (Lin et al., 2003 [PubMed 14595443]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0089 (1355/152270) while in subpopulation NFE AF= 0.0159 (1078/67996). AF 95% confidence interval is 0.0151. There are 6 homozygotes in gnomad4. There are 611 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1355 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC4C | NM_001258419.2 | c.-407+78599A>G | intron_variant | ENST00000528697.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC4C | ENST00000528697.6 | c.-407+78599A>G | intron_variant | 1 | NM_001258419.2 | P1 | |||
LRRC4C | ENST00000530763.5 | c.-326-206758A>G | intron_variant | 1 | P1 | ||||
LRRC4C | ENST00000534577.1 | n.507+78599A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00891 AC: 1355AN: 152152Hom.: 6 Cov.: 33
GnomAD3 genomes
?
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1355
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152152
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00890 AC: 1355AN: 152270Hom.: 6 Cov.: 33 AF XY: 0.00821 AC XY: 611AN XY: 74460
GnomAD4 genome
?
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1355
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33
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611
AN XY:
74460
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7
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3472
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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