chr1-32075014-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001319677.2(TMEM39B):c.-314C>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.0000296 in 1,551,444 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 Uncertain significance (★).
Frequency
Consequence
NM_001319677.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000640 AC: 10AN: 156206Hom.: 0 AF XY: 0.0000604 AC XY: 5AN XY: 82786
GnomAD4 exome AF: 0.0000286 AC: 40AN: 1399284Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 19AN XY: 690158
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.68C>T (p.S23L) alteration is located in exon 2 (coding exon 2) of the TMEM39B gene. This alteration results from a C to T substitution at nucleotide position 68, causing the serine (S) at amino acid position 23 to be replaced by a leucine (L). 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