6-35498383-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_003322.6(TULP1):c.1573C>T(p.Leu525=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,736 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 (★). Synonymous variant affecting the same amino acid position (i.e. L525L) has been classified as Likely benign.
Frequency
Consequence
NM_003322.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TULP1 | NM_003322.6 | c.1573C>T | p.Leu525= | synonymous_variant | 15/15 | ENST00000229771.11 | |
LOC124901309 | XR_007059561.1 | n.75+176G>A | intron_variant, non_coding_transcript_variant | ||||
TULP1 | NM_001289395.2 | c.1414C>T | p.Leu472= | synonymous_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TULP1 | ENST00000229771.11 | c.1573C>T | p.Leu525= | synonymous_variant | 15/15 | 1 | NM_003322.6 | P4 | |
TULP1 | ENST00000322263.8 | c.1414C>T | p.Leu472= | synonymous_variant | 14/14 | 1 | A2 | ||
TULP1 | ENST00000614066.4 | c.1567C>T | p.Leu523= | synonymous_variant | 14/14 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152262Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461474Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727050
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152262Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74388
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at