rs1060504702
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The ENST00000281928.9(MED13L):c.57C>A(p.Ser19=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000066 in 151,552 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0000028 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MED13L
ENST00000281928.9 synonymous
ENST00000281928.9 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.44
Genes affected
MED13L (HGNC:22962): (mediator complex subunit 13L) The protein encoded by this gene is a subunit of the Mediator complex, a large complex of proteins that functions as a transcriptional coactivator for most RNA polymerase II-transcribed genes. The encoded protein is involved in early development of the heart and brain. Defects in this gene are a cause of transposition of the great arteries, dextro-looped (DTGA).[provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
Variant 12-116277075-G-T is Benign according to our data. Variant chr12-116277075-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 415974.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=3.44 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MED13L | NM_015335.5 | c.57C>A | p.Ser19= | synonymous_variant | 1/31 | ENST00000281928.9 | NP_056150.1 | |
MED13L | XM_017019090.2 | c.57C>A | p.Ser19= | synonymous_variant | 1/31 | XP_016874579.1 | ||
MED13L | XM_047428608.1 | c.-108C>A | 5_prime_UTR_variant | 1/30 | XP_047284564.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MED13L | ENST00000281928.9 | c.57C>A | p.Ser19= | synonymous_variant | 1/31 | 1 | NM_015335.5 | ENSP00000281928 | P1 | |
MED13L | ENST00000650226.1 | c.57C>A | p.Ser19= | synonymous_variant | 1/31 | ENSP00000496981 | ||||
MED13L | ENST00000551197.2 | c.9C>A | p.Ser3= | synonymous_variant | 1/4 | 5 | ENSP00000497043 |
Frequencies
GnomAD3 genomes AF: 0.00000660 AC: 1AN: 151552Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.0000141 AC: 3AN: 213250Hom.: 0 AF XY: 0.0000172 AC XY: 2AN XY: 116276
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000278 AC: 4AN: 1439478Hom.: 0 Cov.: 34 AF XY: 0.00000140 AC XY: 1AN XY: 713814
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GnomAD4 genome AF: 0.00000660 AC: 1AN: 151552Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74016
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Transposition of the great arteries, dextro-looped Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 02, 2016 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at