rs7498665
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001387430.1(SH2B1):āc.1450A>Gā(p.Thr484Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 1,565,774 control chromosomes in the GnomAD database, including 114,338 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T484G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001387430.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH2B1 | NM_001387430.1 | c.1450A>G | p.Thr484Ala | missense_variant | 5/8 | ENST00000684370.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH2B1 | ENST00000684370.1 | c.1450A>G | p.Thr484Ala | missense_variant | 5/8 | NM_001387430.1 | P3 |
Frequencies
GnomAD3 genomes AF: 0.346 AC: 50546AN: 146026Hom.: 9247 Cov.: 23
GnomAD3 exomes AF: 0.351 AC: 87551AN: 249400Hom.: 17007 AF XY: 0.343 AC XY: 46316AN XY: 134960
GnomAD4 exome AF: 0.379 AC: 538478AN: 1419620Hom.: 105062 Cov.: 30 AF XY: 0.375 AC XY: 265080AN XY: 707606
GnomAD4 genome AF: 0.346 AC: 50639AN: 146154Hom.: 9276 Cov.: 23 AF XY: 0.345 AC XY: 24546AN XY: 71228
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 19, 2021 | This variant is associated with the following publications: (PMID: 19079261, 21912638, 23818875, 24971614, 23270367) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at