6-30702853-G-A
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014641.3(MDC1):c.5890C>T(p.Pro1964Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014641.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MDC1 | NM_014641.3 | c.5890C>T | p.Pro1964Ser | missense_variant | Exon 13 of 15 | ENST00000376406.8 | NP_055456.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MDC1 | ENST00000376406.8 | c.5890C>T | p.Pro1964Ser | missense_variant | Exon 13 of 15 | 5 | NM_014641.3 | ENSP00000365588.3 | ||
MDC1 | ENST00000489540.1 | n.872C>T | non_coding_transcript_exon_variant | Exon 3 of 5 | 2 | |||||
MDC1-AS1 | ENST00000442150.1 | n.-214G>A | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00000811 AC: 2AN: 246620 AF XY: 0.00000744 show subpopulations
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1460814Hom.: 0 Cov.: 33 AF XY: 0.0000165 AC XY: 12AN XY: 726722 show subpopulations
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74350 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5890C>T (p.P1964S) alteration is located in exon 13 (coding exon 12) of the MDC1 gene. This alteration results from a C to T substitution at nucleotide position 5890, causing the proline (P) at amino acid position 1964 to be replaced by a serine (S). 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