NM_004553.6:c.9G>A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004553.6(NDUFS6):c.9G>A(p.Ala3Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000748 in 1,605,098 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A3A) has been classified as Likely benign.
Frequency
Consequence
NM_004553.6 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NDUFS6 | NM_004553.6 | c.9G>A | p.Ala3Ala | synonymous_variant | Exon 1 of 4 | ENST00000274137.10 | NP_004544.1 | |
MRPL36 | XM_011514080.3 | c.-60C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 2 | XP_011512382.1 | |||
MRPL36 | XM_011514080.3 | c.-60C>T | 5_prime_UTR_variant | Exon 1 of 2 | XP_011512382.1 | |||
MRPL36 | XM_017009751.3 | c.-201C>T | upstream_gene_variant | XP_016865240.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NDUFS6 | ENST00000274137.10 | c.9G>A | p.Ala3Ala | synonymous_variant | Exon 1 of 4 | 1 | NM_004553.6 | ENSP00000274137.6 | ||
NDUFS6 | ENST00000469176.1 | c.9G>A | p.Ala3Ala | synonymous_variant | Exon 1 of 3 | 2 | ENSP00000422557.1 | |||
NDUFS6 | ENST00000510329.1 | n.6G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 | |||||
MRPL36 | ENST00000505818.1 | c.-105C>T | upstream_gene_variant | 3 | ENSP00000427152.1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152254Hom.: 0 Cov.: 36
GnomAD3 exomes AF: 0.0000132 AC: 3AN: 227000Hom.: 0 AF XY: 0.00000793 AC XY: 1AN XY: 126158
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1452844Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 722670
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152254Hom.: 0 Cov.: 36 AF XY: 0.0000941 AC XY: 7AN XY: 74382
ClinVar
Submissions by phenotype
Mitochondrial complex I deficiency Benign:1
- -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at