X-81115003-C-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_030763.3(HMGN5):c.495G>C(p.Glu165Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00037 in 1,148,328 control chromosomes in the GnomAD database, including 1 homozygotes. There are 127 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_030763.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00194 AC: 211AN: 108889Hom.: 0 Cov.: 22 AF XY: 0.00175 AC XY: 55AN XY: 31509
GnomAD3 exomes AF: 0.000450 AC: 46AN: 102175Hom.: 0 AF XY: 0.000311 AC XY: 10AN XY: 32139
GnomAD4 exome AF: 0.000206 AC: 214AN: 1039386Hom.: 1 Cov.: 31 AF XY: 0.000215 AC XY: 72AN XY: 335574
GnomAD4 genome AF: 0.00194 AC: 211AN: 108942Hom.: 0 Cov.: 22 AF XY: 0.00174 AC XY: 55AN XY: 31570
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at