5-174107483-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015980.5(NSG2):c.494C>T(p.Pro165Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00018 in 1,609,578 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_015980.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152184Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000321 AC: 79AN: 246342Hom.: 0 AF XY: 0.000291 AC XY: 39AN XY: 133796
GnomAD4 exome AF: 0.000182 AC: 265AN: 1457394Hom.: 0 Cov.: 31 AF XY: 0.000170 AC XY: 123AN XY: 724100
GnomAD4 genome AF: 0.000164 AC: 25AN: 152184Hom.: 0 Cov.: 31 AF XY: 0.0000807 AC XY: 6AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.494C>T (p.P165L) alteration is located in exon 5 (coding exon 4) of the HMP19 gene. This alteration results from a C to T substitution at nucleotide position 494, causing the proline (P) at amino acid position 165 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