chr19-5654099-A-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001201338.2(SAFB):c.1565A>C(p.Lys522Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00016 in 1,614,080 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001201338.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251478Hom.: 1 AF XY: 0.000103 AC XY: 14AN XY: 135912
GnomAD4 exome AF: 0.000165 AC: 241AN: 1461858Hom.: 1 Cov.: 31 AF XY: 0.000172 AC XY: 125AN XY: 727236
GnomAD4 genome AF: 0.000118 AC: 18AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1565A>C (p.K522T) alteration is located in exon 12 (coding exon 12) of the SAFB gene. This alteration results from a A to C substitution at nucleotide position 1565, causing the lysine (K) at amino acid position 522 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at