20-35699310-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_021100.5(NFS1):c.-22G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000215 in 1,397,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_021100.5 5_prime_UTR
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 |
---|---|---|---|---|---|---|---|---|
NFS1 | NM_021100.5 | c.-22G>A | 5_prime_UTR_variant | Exon 1 of 13 | ENST00000374092.9 | NP_066923.3 | ||
NFS1 | NM_001198989.2 | c.-22G>A | 5_prime_UTR_variant | Exon 1 of 12 | NP_001185918.1 | |||
NFS1 | NR_037570.3 | n.43G>A | non_coding_transcript_exon_variant | Exon 1 of 14 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000186 AC: 4AN: 21498Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 11616
GnomAD4 exome AF: 0.000228 AC: 284AN: 1244668Hom.: 0 Cov.: 30 AF XY: 0.000217 AC XY: 131AN XY: 602384
GnomAD4 genome AF: 0.000105 AC: 16AN: 152346Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74494
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at