rs2273890
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_018662.3(DISC1):c.1689+6T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 1,609,354 control chromosomes in the GnomAD database, including 13,975 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_018662.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DISC1 | ENST00000439617.8 | c.1689+6T>C | splice_region_variant, intron_variant | Intron 7 of 12 | 5 | NM_018662.3 | ENSP00000403888.4 | |||
DISC1 | ENST00000366637.8 | c.1689+6T>C | splice_region_variant, intron_variant | Intron 7 of 12 | 5 | ENSP00000355597.6 | ||||
TSNAX-DISC1 | ENST00000602956.5 | n.*1550+6T>C | splice_region_variant, intron_variant | Intron 11 of 12 | 2 | ENSP00000473532.1 |
Frequencies
GnomAD3 genomes AF: 0.122 AC: 18548AN: 152092Hom.: 1214 Cov.: 32
GnomAD3 exomes AF: 0.115 AC: 28597AN: 247988Hom.: 1830 AF XY: 0.115 AC XY: 15417AN XY: 134356
GnomAD4 exome AF: 0.130 AC: 188813AN: 1457146Hom.: 12757 Cov.: 30 AF XY: 0.128 AC XY: 92653AN XY: 725198
GnomAD4 genome AF: 0.122 AC: 18570AN: 152208Hom.: 1218 Cov.: 32 AF XY: 0.119 AC XY: 8883AN XY: 74398
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at