chr13-30921021-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_032849.4(MEDAG):c.396G>A(p.Thr132=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00226 in 1,613,278 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0017 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0023 ( 7 hom. )
Consequence
MEDAG
NM_032849.4 synonymous
NM_032849.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.31
Genes affected
MEDAG (HGNC:25926): (mesenteric estrogen dependent adipogenesis) Predicted to be involved in positive regulation of fat cell differentiation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 13-30921021-G-A is Benign according to our data. Variant chr13-30921021-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2643712.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.31 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEDAG | NM_032849.4 | c.396G>A | p.Thr132= | synonymous_variant | 3/5 | ENST00000380482.9 | |
TEX26-AS1 | NR_038287.1 | n.1437+9780C>T | intron_variant, non_coding_transcript_variant | ||||
MEDAG | XM_017020801.2 | c.-58G>A | 5_prime_UTR_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEDAG | ENST00000380482.9 | c.396G>A | p.Thr132= | synonymous_variant | 3/5 | 1 | NM_032849.4 | P1 | |
TEX26-AS1 | ENST00000585870.6 | n.1437+9780C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00172 AC: 261AN: 152172Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00216 AC: 541AN: 250652Hom.: 3 AF XY: 0.00219 AC XY: 296AN XY: 135400
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GnomAD4 exome AF: 0.00232 AC: 3387AN: 1460988Hom.: 7 Cov.: 30 AF XY: 0.00228 AC XY: 1656AN XY: 726736
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GnomAD4 genome AF: 0.00171 AC: 261AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.00173 AC XY: 129AN XY: 74460
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | MEDAG: BP4, BP7, BS2; TEX26-AS1: BS2 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at