1-39626914-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_014571.4(HEYL):c.580G>A(p.Ala194Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,610,206 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A194D) has been classified as Uncertain significance.
Frequency
Consequence
NM_014571.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151998Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000528 AC: 13AN: 246128Hom.: 0 AF XY: 0.0000676 AC XY: 9AN XY: 133184
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1458208Hom.: 0 Cov.: 33 AF XY: 0.0000234 AC XY: 17AN XY: 724966
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151998Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74248
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.580G>A (p.A194T) alteration is located in exon 5 (coding exon 5) of the HEYL gene. This alteration results from a G to A substitution at nucleotide position 580, causing the alanine (A) at amino acid position 194 to be replaced by a threonine (T). 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