rs7695038
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_025074.7(FRAS1):c.9116-5C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000368 in 1,612,096 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_025074.7 splice_region, splice_polypyrimidine_tract, 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 | UniProt |
---|---|---|---|---|---|---|---|
FRAS1 | NM_025074.7 | c.9116-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000512123.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRAS1 | ENST00000512123.4 | c.9116-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_025074.7 | P1 | |||
FRAS1 | ENST00000682513.1 | c.9116-5C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 151774Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000838 AC: 208AN: 248282Hom.: 0 AF XY: 0.00115 AC XY: 155AN XY: 134694
GnomAD4 exome AF: 0.000384 AC: 560AN: 1460206Hom.: 4 Cov.: 32 AF XY: 0.000567 AC XY: 412AN XY: 726382
GnomAD4 genome ? AF: 0.000217 AC: 33AN: 151890Hom.: 0 Cov.: 33 AF XY: 0.000337 AC XY: 25AN XY: 74234
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at