7-39566437-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_020192.5(YAE1):c.19G>A(p.Ala7Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000269 in 1,614,168 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020192.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YAE1 | NM_020192.5 | c.19G>A | p.Ala7Thr | missense_variant | 1/3 | ENST00000223273.7 | |
YAE1 | NM_001282446.2 | c.19G>A | p.Ala7Thr | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YAE1 | ENST00000223273.7 | c.19G>A | p.Ala7Thr | missense_variant | 1/3 | 1 | NM_020192.5 | P1 | |
YAE1 | ENST00000432096.2 | c.19G>A | p.Ala7Thr | missense_variant | 1/3 | 2 | |||
YAE1 | ENST00000448268.5 | c.19G>A | p.Ala7Thr | missense_variant | 1/3 | 2 | |||
YAE1 | ENST00000474392.1 | n.53G>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000197 AC: 30AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000263 AC: 66AN: 251384Hom.: 1 AF XY: 0.000294 AC XY: 40AN XY: 135872
GnomAD4 exome AF: 0.000276 AC: 404AN: 1461814Hom.: 4 Cov.: 30 AF XY: 0.000286 AC XY: 208AN XY: 727208
GnomAD4 genome ? AF: 0.000197 AC: 30AN: 152354Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 14, 2023 | The c.19G>A (p.A7T) alteration is located in exon 1 (coding exon 1) of the YAE1D1 gene. This alteration results from a G to A substitution at nucleotide position 19, causing the alanine (A) at amino acid position 7 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