rs7315731
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004719.3(SCAF11):c.1970T>A(p.Phe657Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 1,609,834 control chromosomes in the GnomAD database, including 186,367 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004719.3 missense
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 |
---|---|---|---|---|---|---|---|---|
SCAF11 | NM_004719.3 | c.1970T>A | p.Phe657Tyr | missense_variant | 11/15 | ENST00000369367.8 | NP_004710.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCAF11 | ENST00000369367.8 | c.1970T>A | p.Phe657Tyr | missense_variant | 11/15 | 1 | NM_004719.3 | ENSP00000358374.3 | ||
SCAF11 | ENST00000549162.5 | c.1394T>A | p.Phe465Tyr | missense_variant | 5/9 | 1 | ENSP00000448864.1 | |||
SCAF11 | ENST00000465950.5 | c.1025T>A | p.Phe342Tyr | missense_variant | 1/5 | 1 | ENSP00000449812.1 | |||
SCAF11 | ENST00000547018.5 | n.1790T>A | non_coding_transcript_exon_variant | 11/11 | 5 | ENSP00000446746.1 |
Frequencies
GnomAD3 genomes AF: 0.393 AC: 59706AN: 151870Hom.: 13514 Cov.: 31
GnomAD3 exomes AF: 0.463 AC: 115218AN: 248810Hom.: 27740 AF XY: 0.474 AC XY: 63727AN XY: 134578
GnomAD4 exome AF: 0.483 AC: 704063AN: 1457846Hom.: 172838 Cov.: 38 AF XY: 0.486 AC XY: 352131AN XY: 725250
GnomAD4 genome AF: 0.393 AC: 59732AN: 151988Hom.: 13529 Cov.: 31 AF XY: 0.397 AC XY: 29477AN XY: 74276
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at