chr10-25023767-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024838.5(THNSL1):āc.544A>Gā(p.Met182Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,613,930 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_024838.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THNSL1 | NM_024838.5 | c.544A>G | p.Met182Val | missense_variant | 3/3 | ENST00000376356.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THNSL1 | ENST00000376356.5 | c.544A>G | p.Met182Val | missense_variant | 3/3 | 1 | NM_024838.5 | P1 | |
ENKUR | ENST00000615958.4 | c.38-27898T>C | intron_variant | 1 | |||||
THNSL1 | ENST00000524413.5 | c.544A>G | p.Met182Val | missense_variant | 3/3 | 3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250846Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135654
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461710Hom.: 0 Cov.: 38 AF XY: 0.0000275 AC XY: 20AN XY: 727134
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 06, 2022 | The c.544A>G (p.M182V) alteration is located in exon 3 (coding exon 1) of the THNSL1 gene. This alteration results from a A to G substitution at nucleotide position 544, causing the methionine (M) at amino acid position 182 to be replaced by a valine (V). 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