chr6-46829535-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005588.3(MEP1A):c.1108A>G(p.Asn370Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,614,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005588.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEP1A | NM_005588.3 | c.1108A>G | p.Asn370Asp | missense_variant | 10/14 | ENST00000230588.9 | |
MEP1A | XM_011514628.2 | c.1192A>G | p.Asn398Asp | missense_variant | 9/13 | ||
MEP1A | XM_011514629.3 | c.1108A>G | p.Asn370Asp | missense_variant | 10/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEP1A | ENST00000230588.9 | c.1108A>G | p.Asn370Asp | missense_variant | 10/14 | 1 | NM_005588.3 | P1 | |
MEP1A | ENST00000611727.2 | c.1192A>G | p.Asn398Asp | missense_variant | 9/13 | 1 | |||
MEP1A | ENST00000680769.1 | n.1289A>G | non_coding_transcript_exon_variant | 8/12 | |||||
MEP1A | ENST00000680229.1 | c.*293A>G | 3_prime_UTR_variant, NMD_transcript_variant | 10/14 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152204Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461876Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727240
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2021 | The c.1108A>G (p.N370D) alteration is located in exon 10 (coding exon 10) of the MEP1A gene. This alteration results from a A to G substitution at nucleotide position 1108, causing the asparagine (N) at amino acid position 370 to be replaced by an aspartic acid (D). 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