ENST00000395461.7:c.92T>C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000395461.7(LAT):āc.92T>Cā(p.Leu31Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,612,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000395461.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAT | NM_001014987.2 | c.-17T>C | 5_prime_UTR_variant | Exon 1 of 12 | ENST00000395456.7 | NP_001014987.1 | ||
LAT | NM_001014989.2 | c.92T>C | p.Leu31Pro | missense_variant | Exon 2 of 13 | NP_001014989.2 | ||
LAT | NM_014387.4 | c.-17T>C | 5_prime_UTR_variant | Exon 1 of 11 | NP_055202.1 | |||
LAT | NM_001014988.2 | c.-17T>C | 5_prime_UTR_variant | Exon 1 of 12 | NP_001014988.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152112Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460830Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726752
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.92T>C (p.L31P) alteration is located in exon 2 (coding exon 2) of the LAT gene. This alteration results from a T to C substitution at nucleotide position 92, causing the leucine (L) at amino acid position 31 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at