chr17-3669201-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_031298.4(EMC6):c.55G>T(p.Val19Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000252 in 1,592,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. V19A) has been classified as Uncertain significance.
Frequency
Consequence
NM_031298.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EMC6 | NM_031298.4 | c.55G>T | p.Val19Leu | missense_variant | Exon 2 of 2 | ENST00000248378.6 | NP_112588.1 | |
EMC6 | NM_001014764.3 | c.55G>T | p.Val19Leu | missense_variant | Exon 2 of 2 | NP_001014764.1 | ||
P2RX5-TAX1BP3 | NR_037928.1 | n.4951C>A | non_coding_transcript_exon_variant | Exon 12 of 15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EMC6 | ENST00000248378.6 | c.55G>T | p.Val19Leu | missense_variant | Exon 2 of 2 | 1 | NM_031298.4 | ENSP00000248378.4 | ||
P2RX5-TAX1BP3 | ENST00000550383.1 | n.*3253C>A | non_coding_transcript_exon_variant | Exon 12 of 15 | 2 | ENSP00000455681.1 | ||||
P2RX5-TAX1BP3 | ENST00000550383.1 | n.*3253C>A | 3_prime_UTR_variant | Exon 12 of 15 | 2 | ENSP00000455681.1 | ||||
EMC6 | ENST00000397133.2 | c.55G>T | p.Val19Leu | missense_variant | Exon 2 of 2 | 2 | ENSP00000380322.1 |
Frequencies
GnomAD3 genomes AF: 0.0000919 AC: 14AN: 152274Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000774 AC: 17AN: 219616Hom.: 0 AF XY: 0.000124 AC XY: 15AN XY: 120736
GnomAD4 exome AF: 0.000269 AC: 388AN: 1440628Hom.: 0 Cov.: 31 AF XY: 0.000266 AC XY: 190AN XY: 714770
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152274Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74400
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.55G>T (p.V19L) alteration is located in exon 2 (coding exon 1) of the EMC6 gene. This alteration results from a G to T substitution at nucleotide position 55, causing the valine (V) at amino acid position 19 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