17-5500619-T-C
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001162371.3(LOC728392):c.338A>G(p.Tyr113Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000351 in 1,112,558 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001162371.3 missense
Scores
Clinical Significance
Conservation
Publications
- corneal intraepithelial dyskeratosis-palmoplantar hyperkeratosis-laryngeal dyskeratosis syndromeInheritance: AD, SD Classification: STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, G2P, Ambry Genetics
- autoinflammation with arthritis and dyskeratosisInheritance: AR, SD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC728392 | NM_001162371.3 | c.338A>G | p.Tyr113Cys | missense_variant | Exon 1 of 2 | ENST00000568641.2 | NP_001155843.1 | |
LOC124900388 | XM_047437232.1 | c.-296A>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 2 | XP_047293188.1 | |||
LOC124900388 | XM_047437232.1 | c.-296A>G | 5_prime_UTR_variant | Exon 1 of 2 | XP_047293188.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000286190 | ENST00000568641.2 | c.338A>G | p.Tyr113Cys | missense_variant | Exon 1 of 2 | 1 | NM_001162371.3 | ENSP00000499042.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD2 exomes AF: 0.0000849 AC: 10AN: 117792 AF XY: 0.000142 show subpopulations
GnomAD4 exome AF: 0.0000351 AC: 39AN: 1112558Hom.: 0 Cov.: 30 AF XY: 0.0000569 AC XY: 31AN XY: 544440 show subpopulations
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.338A>G (p.Y113C) alteration is located in exon 1 (coding exon 1) of the LOC728392 gene. This alteration results from a A to G substitution at nucleotide position 338, causing the tyrosine (Y) at amino acid position 113 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