1-37989579-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006802.4(SF3A3):c.113A>G(p.Asn38Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000096 in 1,613,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006802.4 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: 0.000138 AC: 21AN: 152198Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000179 AC: 45AN: 251096Hom.: 0 AF XY: 0.000192 AC XY: 26AN XY: 135736
GnomAD4 exome AF: 0.0000917 AC: 134AN: 1461756Hom.: 0 Cov.: 31 AF XY: 0.000102 AC XY: 74AN XY: 727186
GnomAD4 genome AF: 0.000138 AC: 21AN: 152198Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 12AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.113A>G (p.N38S) alteration is located in exon 2 (coding exon 2) of the SF3A3 gene. This alteration results from a A to G substitution at nucleotide position 113, causing the asparagine (N) at amino acid position 38 to be replaced by a serine (S). 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