5-113027325-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001085377.2(MCC):c.3037C>A(p.His1013Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,614,058 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 Uncertain significance (★).
Frequency
Consequence
NM_001085377.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCC | ENST00000408903.7 | c.3037C>A | p.His1013Asn | missense_variant | Exon 19 of 19 | 2 | NM_001085377.2 | ENSP00000386227.3 | ||
MCC | ENST00000302475.9 | c.2467C>A | p.His823Asn | missense_variant | Exon 17 of 17 | 1 | ENSP00000305617.4 | |||
MCC | ENST00000515367.6 | c.2278C>A | p.His760Asn | missense_variant | Exon 17 of 17 | 5 | ENSP00000421615.2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251304Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135814
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461846Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727224
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3037C>A (p.H1013N) alteration is located in exon 19 (coding exon 19) of the MCC gene. This alteration results from a C to A substitution at nucleotide position 3037, causing the histidine (H) at amino acid position 1013 to be replaced by an asparagine (N). 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