chr2-181678728-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002500.5(NEUROD1):c.133A>G(p.Thr45Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 1,611,182 control chromosomes in the GnomAD database, including 356,278 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 Benign (★★).
Frequency
Consequence
NM_002500.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEUROD1 | NM_002500.5 | c.133A>G | p.Thr45Ala | missense_variant | 2/2 | ENST00000295108.4 | |
NEUROD1 | NR_146175.2 | n.88+1702A>G | intron_variant, non_coding_transcript_variant | ||||
NEUROD1 | NR_146176.2 | n.88+1702A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEUROD1 | ENST00000295108.4 | c.133A>G | p.Thr45Ala | missense_variant | 2/2 | 1 | NM_002500.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.685 AC: 103930AN: 151820Hom.: 36024 Cov.: 30
GnomAD3 exomes AF: 0.702 AC: 173739AN: 247414Hom.: 62114 AF XY: 0.703 AC XY: 94054AN XY: 133770
GnomAD4 exome AF: 0.658 AC: 960681AN: 1459244Hom.: 320216 Cov.: 73 AF XY: 0.663 AC XY: 481242AN XY: 725666
GnomAD4 genome ? AF: 0.685 AC: 104019AN: 151938Hom.: 36062 Cov.: 30 AF XY: 0.692 AC XY: 51363AN XY: 74248
ClinVar
Submissions by phenotype
Maturity-onset diabetes of the young type 6 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Maturity onset diabetes mellitus in young Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Retinal dystrophy Benign:1
Benign, criteria provided, single submitter | research | Dept Of Ophthalmology, Nagoya University | Oct 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at