chr6-144421904-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007124.3(UTRN):c.168G>A(p.Met56Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000224 in 1,612,794 control chromosomes in the GnomAD database, including 1 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M56V) has been classified as Uncertain significance.
Frequency
Consequence
NM_007124.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UTRN | NM_007124.3 | c.168G>A | p.Met56Ile | missense_variant | 4/75 | ENST00000367545.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UTRN | ENST00000367545.8 | c.168G>A | p.Met56Ile | missense_variant | 4/75 | 5 | NM_007124.3 | P1 | |
UTRN | ENST00000421035.2 | c.183G>A | p.Met61Ile | missense_variant | 3/6 | 2 | |||
UTRN | ENST00000628146.2 | c.141G>A | p.Met47Ile | missense_variant | 3/6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000335 AC: 51AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000296 AC: 74AN: 250166Hom.: 0 AF XY: 0.000318 AC XY: 43AN XY: 135298
GnomAD4 exome AF: 0.000214 AC: 312AN: 1460524Hom.: 1 Cov.: 30 AF XY: 0.000212 AC XY: 154AN XY: 726564
GnomAD4 genome AF: 0.000328 AC: 50AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.168G>A (p.M56I) alteration is located in exon 3 (coding exon 3) of the UTRN gene. This alteration results from a G to A substitution at nucleotide position 168, causing the methionine (M) at amino acid position 56 to be replaced by an isoleucine (I). 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