21-37625491-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002240.5(KCNJ6):c.947-7T>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 0.0000473 in 1,605,910 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002240.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNJ6 | NM_002240.5 | c.947-7T>C | splice_region_variant, intron_variant | ENST00000609713.2 | NP_002231.1 | |||
KCNJ6-AS1 | NR_183540.1 | n.408-73064A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNJ6 | ENST00000609713.2 | c.947-7T>C | splice_region_variant, intron_variant | 1 | NM_002240.5 | ENSP00000477437.1 | ||||
KCNJ6 | ENST00000645093.1 | c.947-7T>C | splice_region_variant, intron_variant | ENSP00000493772.1 | ||||||
ENSG00000286717 | ENST00000667151.1 | n.161-21056A>G | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000536 AC: 13AN: 242320Hom.: 0 AF XY: 0.0000685 AC XY: 9AN XY: 131474
GnomAD4 exome AF: 0.0000482 AC: 70AN: 1453678Hom.: 0 Cov.: 31 AF XY: 0.0000540 AC XY: 39AN XY: 722690
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74386
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at