9-133341510-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_133640.5(MED22):​c.598G>A​(p.Ala200Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000596 in 1,510,652 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★).

Frequency

Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000059 ( 0 hom. )

Consequence

MED22
NM_133640.5 missense

Scores

2
17

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.38
Variant links:
Genes affected
MED22 (HGNC:11477): (mediator complex subunit 22) This gene encodes a protein component of the mediator complex, which functions in the regulation of transcription by bridging interactions between gene-specific regulatory factors, RNA polymerase II, and general transcription factors. Alternatively spliced transcript variants encoding different isoforms have been observed. [provided by RefSeq, Jul 2013]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.015460998).
BP6
Variant 9-133341510-C-T is Benign according to our data. Variant chr9-133341510-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3394636.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MED22NM_133640.5 linkc.598G>A p.Ala200Thr missense_variant Exon 5 of 5 ENST00000343730.10 NP_598395.1 Q15528-1A0A024R8C5
MED22NM_181491.3 linkc.*2605G>A 3_prime_UTR_variant Exon 4 of 4 NP_852468.1 Q15528-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MED22ENST00000343730.10 linkc.598G>A p.Ala200Thr missense_variant Exon 5 of 5 1 NM_133640.5 ENSP00000342343.5 Q15528-1
MED22ENST00000610888 linkc.*2605G>A 3_prime_UTR_variant Exon 4 of 4 1 ENSP00000478773.1 Q15528-2
MED22ENST00000614493 linkc.*2605G>A 3_prime_UTR_variant Exon 4 of 4 2 ENSP00000481493.1 Q15528-2
MED22ENST00000610672.4 linkc.598G>A p.Ala200Thr missense_variant Exon 5 of 5 2 ENSP00000482438.1 Q15528-1

Frequencies

GnomAD3 genomes
AF:
0.0000657
AC:
10
AN:
152208
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000541
AC:
9
AN:
166434
Hom.:
0
AF XY:
0.0000539
AC XY:
5
AN XY:
92736
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.000170
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000531
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000832
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000589
AC:
80
AN:
1358444
Hom.:
0
Cov.:
29
AF XY:
0.0000611
AC XY:
41
AN XY:
671316
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000289
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000690
Gnomad4 OTH exome
AF:
0.0000717
GnomAD4 genome
AF:
0.0000657
AC:
10
AN:
152208
Hom.:
0
Cov.:
32
AF XY:
0.0000538
AC XY:
4
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000453
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.0000412
AC:
5

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Dec 05, 2024
Ambry Genetics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.078
BayesDel_addAF
Benign
-0.47
T
BayesDel_noAF
Benign
-0.71
CADD
Benign
1.1
DANN
Uncertain
1.0
DEOGEN2
Benign
0.017
T;T
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.1
FATHMM_MKL
Benign
0.042
N
LIST_S2
Benign
0.77
.;T
M_CAP
Benign
0.076
D
MetaRNN
Benign
0.015
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.4
L;L
PrimateAI
Benign
0.37
T
PROVEAN
Benign
-0.18
.;N
REVEL
Benign
0.059
Sift
Benign
0.55
.;T
Sift4G
Uncertain
0.035
D;D
Polyphen
0.0
B;B
Vest4
0.030
MVP
0.15
ClinPred
0.12
T
GERP RS
-0.22
Varity_R
0.016
gMVP
0.20

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs377187824; hg19: chr9-136208360; API