chr9-127843128-A-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001114753.3(ENG):c.185T>A(p.Leu62His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001114753.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENG | NM_001114753.3 | c.185T>A | p.Leu62His | missense_variant | 2/15 | ENST00000373203.9 | |
ENG | NM_000118.4 | c.185T>A | p.Leu62His | missense_variant | 2/14 | ||
ENG | NM_001406715.1 | c.185T>A | p.Leu62His | missense_variant | 2/8 | ||
ENG | NM_001278138.2 | c.-362T>A | 5_prime_UTR_variant | 2/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENG | ENST00000373203.9 | c.185T>A | p.Leu62His | missense_variant | 2/15 | 1 | NM_001114753.3 | P2 | |
ENG | ENST00000344849.4 | c.185T>A | p.Leu62His | missense_variant | 2/14 | 1 | A2 | ||
ENG | ENST00000480266.6 | c.-362T>A | 5_prime_UTR_variant | 2/15 | 2 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251420Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135880
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461862Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 727230
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
Hereditary hemorrhagic telangiectasia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at