6-89664564-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014611.3(MDN1):āc.14159T>Cā(p.Ile4720Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0389 in 1,613,510 control chromosomes in the GnomAD database, including 1,834 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_014611.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MDN1 | NM_014611.3 | c.14159T>C | p.Ile4720Thr | missense_variant | 85/102 | ENST00000369393.8 | |
MDN1-AS1 | NR_111915.1 | n.106-10832A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MDN1 | ENST00000369393.8 | c.14159T>C | p.Ile4720Thr | missense_variant | 85/102 | 1 | NM_014611.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0343 AC: 5222AN: 152170Hom.: 129 Cov.: 32
GnomAD3 exomes AF: 0.0490 AC: 12320AN: 251180Hom.: 473 AF XY: 0.0525 AC XY: 7124AN XY: 135774
GnomAD4 exome AF: 0.0394 AC: 57561AN: 1461222Hom.: 1708 Cov.: 30 AF XY: 0.0420 AC XY: 30499AN XY: 726944
GnomAD4 genome AF: 0.0343 AC: 5226AN: 152288Hom.: 126 Cov.: 32 AF XY: 0.0365 AC XY: 2720AN XY: 74454
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
MDN1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 10, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at