7-36396278-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_018685.5(ANLN):c.31C>T(p.Arg11*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000347 in 1,600,342 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_018685.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANLN | NM_018685.5 | c.31C>T | p.Arg11* | stop_gained | Exon 2 of 24 | ENST00000265748.7 | NP_061155.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANLN | ENST00000265748.7 | c.31C>T | p.Arg11* | stop_gained | Exon 2 of 24 | 1 | NM_018685.5 | ENSP00000265748.2 | ||
ANLN | ENST00000396068.6 | c.31C>T | p.Arg11* | stop_gained | Exon 2 of 23 | 1 | ENSP00000379380.2 | |||
ANLN | ENST00000424865 | c.-36C>T | 5_prime_UTR_variant | Exon 2 of 4 | 3 | ENSP00000404979.1 | ||||
ANLN | ENST00000418118 | c.-36C>T | 5_prime_UTR_variant | Exon 2 of 2 | 3 | ENSP00000406584.1 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000174 AC: 43AN: 247404Hom.: 0 AF XY: 0.000179 AC XY: 24AN XY: 133792
GnomAD4 exome AF: 0.000359 AC: 520AN: 1448258Hom.: 0 Cov.: 30 AF XY: 0.000374 AC XY: 269AN XY: 720088
GnomAD4 genome AF: 0.000230 AC: 35AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74278
ClinVar
Submissions by phenotype
Focal segmental glomerulosclerosis 8 Uncertain:2Other:1
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Variant interpretted as Uncertain significance and reported on 07/26/2017 by GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
not provided Uncertain:2
This sequence change creates a premature translational stop signal (p.Arg11*) in the ANLN gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in ANLN cause disease. This variant is present in population databases (rs200989750, gnomAD 0.06%), and has an allele count higher than expected for a pathogenic variant. This premature translational stop signal has been observed in individual(s) with focal segmental glomerulosclerosis (PMID: 29869118). ClinVar contains an entry for this variant (Variation ID: 599127). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at