20-35672750-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_021100.5(NFS1):c.1310+5A>G variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000157 in 1,585,638 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_021100.5 splice_donor_5th_base, intron
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFS1 | NM_021100.5 | c.1310+5A>G | splice_donor_5th_base_variant, intron_variant | ENST00000374092.9 | |||
NFS1 | NM_001198989.2 | c.1157+5A>G | splice_donor_5th_base_variant, intron_variant | ||||
NFS1 | NR_037570.3 | n.1496+5A>G | splice_donor_5th_base_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFS1 | ENST00000374092.9 | c.1310+5A>G | splice_donor_5th_base_variant, intron_variant | 1 | NM_021100.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000231 AC: 58AN: 251280Hom.: 0 AF XY: 0.000250 AC XY: 34AN XY: 135834
GnomAD4 exome AF: 0.000162 AC: 232AN: 1433452Hom.: 1 Cov.: 26 AF XY: 0.000165 AC XY: 118AN XY: 714966
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74338
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at