chr15-73052778-A-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000261908.11(NEO1):c.103A>T(p.Arg35Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000305 in 1,164,090 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000261908.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEO1 | NM_002499.4 | c.103A>T | p.Arg35Trp | missense_variant | 1/29 | ENST00000261908.11 | NP_002490.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEO1 | ENST00000261908.11 | c.103A>T | p.Arg35Trp | missense_variant | 1/29 | 1 | NM_002499.4 | ENSP00000261908.6 | ||
NEO1 | ENST00000558964.5 | c.103A>T | p.Arg35Trp | missense_variant | 1/28 | 1 | ENSP00000453200.1 | |||
NEO1 | ENST00000560262.5 | c.103A>T | p.Arg35Trp | missense_variant | 1/28 | 1 | ENSP00000453317.1 | |||
NEO1 | ENST00000339362.9 | c.103A>T | p.Arg35Trp | missense_variant | 2/30 | 5 | ENSP00000341198.5 |
Frequencies
GnomAD3 genomes AF: 0.00161 AC: 230AN: 143302Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.000190 AC: 5AN: 26310Hom.: 0 AF XY: 0.000124 AC XY: 2AN XY: 16176
GnomAD4 exome AF: 0.000122 AC: 125AN: 1020636Hom.: 2 Cov.: 20 AF XY: 0.000113 AC XY: 56AN XY: 496114
GnomAD4 genome AF: 0.00160 AC: 230AN: 143454Hom.: 0 Cov.: 29 AF XY: 0.00151 AC XY: 106AN XY: 69974
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.103A>T (p.R35W) alteration is located in exon 1 (coding exon 1) of the NEO1 gene. This alteration results from a A to T substitution at nucleotide position 103, causing the arginine (R) at amino acid position 35 to be replaced by a tryptophan (W). 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