5-126485737-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_023927.4(GRAMD2B):c.1022C>T(p.Pro341Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000109 in 1,611,480 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_023927.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRAMD2B | NM_023927.4 | c.1022C>T | p.Pro341Leu | missense_variant | 11/14 | ENST00000285689.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRAMD2B | ENST00000285689.8 | c.1022C>T | p.Pro341Leu | missense_variant | 11/14 | 1 | NM_023927.4 | P1 | |
ENST00000648070.1 | n.705-18106G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000184 AC: 46AN: 250190Hom.: 0 AF XY: 0.000192 AC XY: 26AN XY: 135308
GnomAD4 exome AF: 0.000110 AC: 160AN: 1459226Hom.: 0 Cov.: 28 AF XY: 0.000107 AC XY: 78AN XY: 726098
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74456
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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