6-149918238-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001001788.4(RAET1G):c.778C>T(p.Pro260Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,614,068 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 Uncertain significance (★).
Frequency
Consequence
NM_001001788.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAET1G | NM_001001788.4 | c.778C>T | p.Pro260Ser | missense_variant | 4/5 | ENST00000367360.7 | NP_001001788.2 | |
RAET1E-AS1 | NR_045126.1 | n.886-949G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAET1G | ENST00000367360.7 | c.778C>T | p.Pro260Ser | missense_variant | 4/5 | 1 | NM_001001788.4 | ENSP00000356329 | P2 | |
RAET1E-AS1 | ENST00000605899.1 | n.115-949G>A | intron_variant, non_coding_transcript_variant | 5 | ||||||
RAET1E-AS1 | ENST00000606915.1 | n.890-949G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251414Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135894
GnomAD4 exome AF: 0.000107 AC: 156AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.000105 AC XY: 76AN XY: 727246
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2024 | The c.778C>T (p.P260S) alteration is located in exon 4 (coding exon 4) of the RAET1G gene. This alteration results from a C to T substitution at nucleotide position 778, causing the proline (P) at amino acid position 260 to be replaced by a serine (S). 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