6-160029591-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_000876.4(IGF2R):c.818A>G(p.Asp273Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000452 in 1,613,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGF2R | NM_000876.4 | c.818A>G | p.Asp273Gly | missense_variant | 7/48 | ENST00000356956.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGF2R | ENST00000356956.6 | c.818A>G | p.Asp273Gly | missense_variant | 7/48 | 1 | NM_000876.4 | P1 | |
IGF2R | ENST00000677704.1 | c.818A>G | p.Asp273Gly | missense_variant, NMD_transcript_variant | 7/49 | ||||
IGF2R | ENST00000676781.1 | c.818A>G | p.Asp273Gly | missense_variant, NMD_transcript_variant | 7/49 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251442Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135888
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461832Hom.: 0 Cov.: 29 AF XY: 0.0000330 AC XY: 24AN XY: 727222
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152162Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | The c.818A>G (p.D273G) alteration is located in exon 7 (coding exon 7) of the IGF2R gene. This alteration results from a A to G substitution at nucleotide position 818, causing the aspartic acid (D) at amino acid position 273 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at