chr15-34228558-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PP3_StrongBS2
The NM_016454.4(EMC4):c.485C>T(p.Ser162Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,461,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016454.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EMC4 | NM_016454.4 | c.485C>T | p.Ser162Leu | missense_variant | Exon 4 of 5 | ENST00000267750.9 | NP_057538.1 | |
EMC4 | NM_001351373.2 | c.242C>T | p.Ser81Leu | missense_variant | Exon 4 of 5 | NP_001338302.1 | ||
EMC4 | NM_001286420.2 | c.355+712C>T | intron_variant | Intron 3 of 3 | NP_001273349.1 | |||
EMC4 | NR_147140.2 | n.462+712C>T | intron_variant | Intron 3 of 3 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461616Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727110
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.485C>T (p.S162L) alteration is located in exon 4 (coding exon 4) of the EMC4 gene. This alteration results from a C to T substitution at nucleotide position 485, causing the serine (S) at amino acid position 162 to be replaced by a leucine (L). 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