NM_001164507.2:c.*201A>T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001164507.2(NEB):c.*201A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00314 in 430,904 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001164507.2 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345 | c.*201A>T | 3_prime_UTR_variant | Exon 182 of 182 | 5 | NM_001164508.2 | ENSP00000380505.3 | |||
NEB | ENST00000427231 | c.*201A>T | 3_prime_UTR_variant | Exon 182 of 182 | 5 | NM_001164507.2 | ENSP00000416578.2 |
Frequencies
GnomAD3 genomes AF: 0.00293 AC: 446AN: 152220Hom.: 4 Cov.: 32
GnomAD4 exome AF: 0.00326 AC: 909AN: 278566Hom.: 7 Cov.: 4 AF XY: 0.00328 AC XY: 467AN XY: 142420
GnomAD4 genome AF: 0.00293 AC: 446AN: 152338Hom.: 4 Cov.: 32 AF XY: 0.00333 AC XY: 248AN XY: 74498
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
not provided Benign:1
NEB: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at