rs1204399
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000373020.9(TSPAN6):c.669+652A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 110,242 control chromosomes in the GnomAD database, including 9,130 homozygotes. There are 14,655 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000373020.9 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSPAN6 | NM_003270.4 | c.669+652A>G | intron_variant | ENST00000373020.9 | NP_003261.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSPAN6 | ENST00000373020.9 | c.669+652A>G | intron_variant | 1 | NM_003270.4 | ENSP00000362111 | P1 | |||
TSPAN6 | ENST00000612152.4 | c.322-967A>G | intron_variant | 5 | ENSP00000482130 |
Frequencies
GnomAD3 genomes AF: 0.462 AC: 50953AN: 110190Hom.: 9125 Cov.: 22 AF XY: 0.450 AC XY: 14623AN XY: 32470
GnomAD4 genome AF: 0.463 AC: 50995AN: 110242Hom.: 9130 Cov.: 22 AF XY: 0.450 AC XY: 14655AN XY: 32532
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at