chr15-32030549-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The XM_047433397.1(LOC124903441):c.40+8C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00438 in 1,442,078 control chromosomes in the GnomAD database, including 239 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
XM_047433397.1 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA7 | NM_000746.6 | c.-46G>T | 5_prime_UTR_variant | 1/10 | ENST00000306901.9 | ||
LOC124903441 | XM_047433397.1 | c.40+8C>A | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA7 | ENST00000306901.9 | c.-46G>T | 5_prime_UTR_variant | 1/10 | 1 | NM_000746.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0225 AC: 3422AN: 151864Hom.: 139 Cov.: 31
GnomAD3 exomes AF: 0.00223 AC: 131AN: 58760Hom.: 3 AF XY: 0.00186 AC XY: 63AN XY: 33854
GnomAD4 exome AF: 0.00224 AC: 2896AN: 1290108Hom.: 100 Cov.: 31 AF XY: 0.00189 AC XY: 1196AN XY: 632902
GnomAD4 genome ? AF: 0.0225 AC: 3426AN: 151970Hom.: 139 Cov.: 31 AF XY: 0.0211 AC XY: 1571AN XY: 74282
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 14, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at