9-70140256-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153267.5(MAMDC2):āc.1106T>Cā(p.Met369Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000162 in 1,601,920 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_153267.5 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 |
---|---|---|---|---|---|---|---|
MAMDC2 | NM_153267.5 | c.1106T>C | p.Met369Thr | missense_variant | 8/14 | ENST00000377182.5 | |
MAMDC2 | NM_001347990.2 | c.1106T>C | p.Met369Thr | missense_variant | 8/12 | ||
MAMDC2 | NR_125850.1 | n.1723T>C | non_coding_transcript_exon_variant | 8/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAMDC2 | ENST00000377182.5 | c.1106T>C | p.Met369Thr | missense_variant | 8/14 | 1 | NM_153267.5 | P1 | |
MAMDC2-AS1 | ENST00000591368.5 | n.408+7725A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000792 AC: 19AN: 239888Hom.: 0 AF XY: 0.0000769 AC XY: 10AN XY: 130030
GnomAD4 exome AF: 0.0000131 AC: 19AN: 1449616Hom.: 0 Cov.: 31 AF XY: 0.0000125 AC XY: 9AN XY: 720916
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152304Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.1106T>C (p.M369T) alteration is located in exon 8 (coding exon 8) of the MAMDC2 gene. This alteration results from a T to C substitution at nucleotide position 1106, causing the methionine (M) at amino acid position 369 to be replaced by a threonine (T). 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