X-140783739-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NR_173139.1(LINC00632):n.909C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000438 in 1,209,135 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NR_173139.1 non_coding_transcript_exon
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LINC00632 | NR_173139.1 | n.909C>T | non_coding_transcript_exon_variant | Exon 5 of 5 | ||||
LINC00632 | NR_173140.2 | n.1016C>T | non_coding_transcript_exon_variant | Exon 5 of 5 | ||||
LINC00632 | NR_173141.1 | n.652C>T | non_coding_transcript_exon_variant | Exon 2 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LINC00632 | ENST00000625883.2 | n.652C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 6 | |||||
LINC00632 | ENST00000648200.2 | n.11758C>T | non_coding_transcript_exon_variant | Exon 5 of 5 | ||||||
LINC00632 | ENST00000648347.1 | n.448C>T | non_coding_transcript_exon_variant | Exon 1 of 2 |
Frequencies
GnomAD3 genomes AF: 0.0000897 AC: 10AN: 111445Hom.: 0 Cov.: 24 AF XY: 0.0000594 AC XY: 2AN XY: 33693
GnomAD3 exomes AF: 0.0000657 AC: 12AN: 182561Hom.: 0 AF XY: 0.0000298 AC XY: 2AN XY: 67099
GnomAD4 exome AF: 0.0000392 AC: 43AN: 1097638Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 7AN XY: 363056
GnomAD4 genome AF: 0.0000897 AC: 10AN: 111497Hom.: 0 Cov.: 24 AF XY: 0.0000593 AC XY: 2AN XY: 33755
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.628G>A (p.G210R) alteration is located in exon 1 (coding exon 1) of the CDR1 gene. This alteration results from a G to A substitution at nucleotide position 628, causing the glycine (G) at amino acid position 210 to be replaced by an arginine (R). 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