11-2133092-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_000612.6(IGF2):c.438C>T(p.Leu146=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,607,802 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 (★). Synonymous variant affecting the same amino acid position (i.e. L146L) has been classified as Likely benign.
Frequency
Consequence
NM_000612.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGF2 | NM_000612.6 | c.438C>T | p.Leu146= | synonymous_variant | 4/4 | ENST00000416167.7 | |
INS-IGF2 | NR_003512.4 | n.1152C>T | non_coding_transcript_exon_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGF2 | ENST00000416167.7 | c.438C>T | p.Leu146= | synonymous_variant | 4/4 | 1 | NM_000612.6 | P4 | |
ENST00000643349.2 | c.*490C>T | 3_prime_UTR_variant | 5/5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244172Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132756
GnomAD4 exome AF: 0.0000158 AC: 23AN: 1455596Hom.: 0 Cov.: 31 AF XY: 0.0000166 AC XY: 12AN XY: 723500
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 16, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at