1-218441356-C-T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_003238.6(TGFB2):c.1239C>T(p.Cys413Cys) variant causes a synonymous change. The variant allele was found at a frequency of 0.000596 in 1,597,108 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003238.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TGFB2 | NM_003238.6 | c.1239C>T | p.Cys413Cys | synonymous_variant | Exon 7 of 7 | ENST00000366930.9 | NP_003229.1 | |
TGFB2 | NM_001135599.4 | c.1323C>T | p.Cys441Cys | synonymous_variant | Exon 8 of 8 | NP_001129071.1 | ||
TGFB2 | NR_138148.2 | n.2490C>T | non_coding_transcript_exon_variant | Exon 7 of 7 | ||||
TGFB2 | NR_138149.2 | n.2574C>T | non_coding_transcript_exon_variant | Exon 8 of 8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TGFB2 | ENST00000366930.9 | c.1239C>T | p.Cys413Cys | synonymous_variant | Exon 7 of 7 | 1 | NM_003238.6 | ENSP00000355897.4 | ||
TGFB2 | ENST00000366929.4 | c.1323C>T | p.Cys441Cys | synonymous_variant | Exon 8 of 8 | 1 | ENSP00000355896.4 | |||
TGFB2 | ENST00000479322.1 | n.723C>T | non_coding_transcript_exon_variant | Exon 5 of 5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00319 AC: 486AN: 152118Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000740 AC: 172AN: 232416Hom.: 1 AF XY: 0.000564 AC XY: 71AN XY: 125788
GnomAD4 exome AF: 0.000322 AC: 465AN: 1444872Hom.: 3 Cov.: 31 AF XY: 0.000291 AC XY: 209AN XY: 718340
GnomAD4 genome AF: 0.00320 AC: 487AN: 152236Hom.: 3 Cov.: 32 AF XY: 0.00304 AC XY: 226AN XY: 74428
ClinVar
Submissions by phenotype
not specified Benign:4
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not provided Benign:4
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TGFB2: BP4, BS1, BS2 -
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Loeys-Dietz syndrome 4 Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at