chr15-77458439-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001304505.2(HMG20A):c.-220C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000415 in 1,613,194 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001304505.2 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: 0.000118 AC: 18AN: 152008Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251222Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135770
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461068Hom.: 1 Cov.: 29 AF XY: 0.0000344 AC XY: 25AN XY: 726862
GnomAD4 genome AF: 0.000118 AC: 18AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.32C>T (p.P11L) alteration is located in exon 3 (coding exon 1) of the HMG20A gene. This alteration results from a C to T substitution at nucleotide position 32, causing the proline (P) at amino acid position 11 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