chr6-160061897-C-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000876.4(IGF2R):āc.3551C>Gā(p.Thr1184Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00174 in 1,614,126 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000876.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGF2R | NM_000876.4 | c.3551C>G | p.Thr1184Ser | missense_variant | 25/48 | ENST00000356956.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGF2R | ENST00000356956.6 | c.3551C>G | p.Thr1184Ser | missense_variant | 25/48 | 1 | NM_000876.4 | P1 | |
IGF2R | ENST00000650503.1 | n.161C>G | non_coding_transcript_exon_variant | 2/24 | |||||
IGF2R | ENST00000677704.1 | c.3551C>G | p.Thr1184Ser | missense_variant, NMD_transcript_variant | 25/49 | ||||
IGF2R | ENST00000676781.1 | c.*1659C>G | 3_prime_UTR_variant, NMD_transcript_variant | 26/49 |
Frequencies
GnomAD3 genomes AF: 0.00924 AC: 1405AN: 152122Hom.: 26 Cov.: 33
GnomAD3 exomes AF: 0.00242 AC: 609AN: 251458Hom.: 6 AF XY: 0.00167 AC XY: 227AN XY: 135904
GnomAD4 exome AF: 0.000958 AC: 1401AN: 1461886Hom.: 21 Cov.: 32 AF XY: 0.000781 AC XY: 568AN XY: 727246
GnomAD4 genome AF: 0.00923 AC: 1405AN: 152240Hom.: 26 Cov.: 33 AF XY: 0.00893 AC XY: 665AN XY: 74454
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at