7-20140999-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_182762.4(MACC1):c.2506A>C(p.Asn836His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000489 in 1,614,012 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_182762.4 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 |
---|---|---|---|---|---|---|---|
MACC1 | NM_182762.4 | c.2506A>C | p.Asn836His | missense_variant | 7/7 | ENST00000400331.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MACC1 | ENST00000400331.10 | c.2506A>C | p.Asn836His | missense_variant | 7/7 | 2 | NM_182762.4 | P1 | |
MACC1 | ENST00000332878.8 | c.2506A>C | p.Asn836His | missense_variant | 5/5 | 1 | P1 | ||
MACC1 | ENST00000589011.1 | c.2506A>C | p.Asn836His | missense_variant | 5/5 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251304Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135832
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461790Hom.: 0 Cov.: 32 AF XY: 0.0000701 AC XY: 51AN XY: 727188
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74430
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 30, 2023 | The c.2506A>C (p.N836H) alteration is located in exon 7 (coding exon 4) of the MACC1 gene. This alteration results from a A to C substitution at nucleotide position 2506, causing the asparagine (N) at amino acid position 836 to be replaced by a histidine (H). 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