chr21-39345211-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004965.7(HMGN1):c.190G>A(p.Glu64Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000338 in 1,613,594 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004965.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000296 AC: 45AN: 152008Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000410 AC: 103AN: 251146Hom.: 1 AF XY: 0.000457 AC XY: 62AN XY: 135790
GnomAD4 exome AF: 0.000342 AC: 500AN: 1461468Hom.: 2 Cov.: 33 AF XY: 0.000363 AC XY: 264AN XY: 727040
GnomAD4 genome AF: 0.000296 AC: 45AN: 152126Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.190G>A (p.E64K) alteration is located in exon 5 (coding exon 5) of the HMGN1 gene. This alteration results from a G to A substitution at nucleotide position 190, causing the glutamic acid (E) at amino acid position 64 to be replaced by a lysine (K). 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