rs147883884
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_206933.4(USH2A):āc.6041A>Cā(p.Asn2014Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000447 in 1,613,936 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 Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N2014K) has been classified as Uncertain significance.
Frequency
Consequence
NM_206933.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.6041A>C | p.Asn2014Thr | missense_variant | 30/72 | ENST00000307340.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.6041A>C | p.Asn2014Thr | missense_variant | 30/72 | 1 | NM_206933.4 | P1 | |
USH2A | ENST00000674083.1 | c.6041A>C | p.Asn2014Thr | missense_variant | 30/73 |
Frequencies
GnomAD3 genomes ? AF: 0.00250 AC: 381AN: 152168Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000689 AC: 173AN: 251182Hom.: 1 AF XY: 0.000508 AC XY: 69AN XY: 135756
GnomAD4 exome AF: 0.000231 AC: 338AN: 1461650Hom.: 2 Cov.: 32 AF XY: 0.000190 AC XY: 138AN XY: 727122
GnomAD4 genome ? AF: 0.00251 AC: 383AN: 152286Hom.: 2 Cov.: 32 AF XY: 0.00254 AC XY: 189AN XY: 74458
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 11, 2012 | This variant is not expected to have clinical significance because it has been i dentified in 23/4552 (0.5%) control chromosomes from a broad, though clinically and racially unspecified population (dbSNP rs147883884) and the variant occurs a t an amino acid position that is poorly conserved with Thr present in most mamma ls. - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 12, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 06, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Retinitis pigmentosa 39 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 04, 2023 | - - |
Usher syndrome type 2A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 04, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at