chr6-6649634-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_004271.4(LY86):c.362A>G(p.Tyr121Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00149 in 1,566,798 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004271.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LY86 | NM_004271.4 | c.362A>G | p.Tyr121Cys | missense_variant | 4/5 | ENST00000230568.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LY86 | ENST00000230568.5 | c.362A>G | p.Tyr121Cys | missense_variant | 4/5 | 1 | NM_004271.4 | P1 | |
LY86 | ENST00000379953.6 | c.362A>G | p.Tyr121Cys | missense_variant | 5/6 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00111 AC: 169AN: 152236Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00105 AC: 253AN: 242014Hom.: 0 AF XY: 0.00104 AC XY: 136AN XY: 130822
GnomAD4 exome AF: 0.00153 AC: 2163AN: 1414444Hom.: 4 Cov.: 25 AF XY: 0.00151 AC XY: 1067AN XY: 705952
GnomAD4 genome ? AF: 0.00111 AC: 169AN: 152354Hom.: 0 Cov.: 34 AF XY: 0.00103 AC XY: 77AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 28, 2022 | The c.362A>G (p.Y121C) alteration is located in exon 4 (coding exon 4) of the LY86 gene. This alteration results from a A to G substitution at nucleotide position 362, causing the tyrosine (Y) at amino acid position 121 to be replaced by a cysteine (C). 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