chr19-16577021-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The ENST00000263390.8(MED26):c.809G>A(p.Arg270His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000404 in 1,608,452 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000263390.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MED26 | NM_004831.5 | c.809G>A | p.Arg270His | missense_variant | 3/3 | ENST00000263390.8 | NP_004822.2 | |
LOC105372295 | XR_936359.3 | n.475-1145C>T | intron_variant | |||||
LOC105372295 | XR_936360.3 | n.260-1145C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MED26 | ENST00000263390.8 | c.809G>A | p.Arg270His | missense_variant | 3/3 | 1 | NM_004831.5 | ENSP00000263390.3 | ||
MED26 | ENST00000611692.4 | c.*174G>A | 3_prime_UTR_variant | 4/4 | 1 | ENSP00000484490.1 | ||||
ENSG00000141979 | ENST00000409035.1 | n.833G>A | non_coding_transcript_exon_variant | 4/12 | 2 | ENSP00000386951.2 | ||||
MED26 | ENST00000597244.1 | n.1757G>A | non_coding_transcript_exon_variant | 1/1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.00209 AC: 318AN: 152230Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.000872 AC: 214AN: 245470Hom.: 6 AF XY: 0.000684 AC XY: 91AN XY: 133054
GnomAD4 exome AF: 0.000229 AC: 333AN: 1456104Hom.: 8 Cov.: 32 AF XY: 0.000213 AC XY: 154AN XY: 723434
GnomAD4 genome AF: 0.00208 AC: 317AN: 152348Hom.: 9 Cov.: 32 AF XY: 0.00299 AC XY: 223AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 15, 2021 | The c.809G>A (p.R270H) alteration is located in exon 3 (coding exon 3) of the MED26 gene. This alteration results from a G to A substitution at nucleotide position 809, causing the arginine (R) at amino acid position 270 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