5-157139217-A-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004270.5(MED7):c.215T>A(p.Phe72Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000657 in 1,612,748 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004270.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MED7 | ENST00000286317.6 | c.215T>A | p.Phe72Tyr | missense_variant | 2/2 | 1 | NM_004270.5 | ENSP00000286317.5 | ||
MED7 | ENST00000420343.1 | c.215T>A | p.Phe72Tyr | missense_variant | 2/2 | 2 | ENSP00000401046.1 | |||
MED7 | ENST00000524289.1 | c.215T>A | p.Phe72Tyr | missense_variant | 3/3 | 3 | ENSP00000430746.1 | |||
HAVCR2 | ENST00000524219.2 | c.-294+3603T>A | intron_variant | 4 | ENSP00000430328.2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152250Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000136 AC: 34AN: 250064Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135220
GnomAD4 exome AF: 0.0000698 AC: 102AN: 1460498Hom.: 1 Cov.: 32 AF XY: 0.0000950 AC XY: 69AN XY: 726594
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 11, 2024 | The c.215T>A (p.F72Y) alteration is located in exon 2 (coding exon 1) of the MED7 gene. This alteration results from a T to A substitution at nucleotide position 215, causing the phenylalanine (F) at amino acid position 72 to be replaced by a tyrosine (Y). 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