7-20784838-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_182700.6(SP8):c.979G>A(p.Ala327Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000343 in 1,525,688 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A327G) has been classified as Uncertain significance.
Frequency
Consequence
NM_182700.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000302 AC: 46AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000257 AC: 31AN: 120526Hom.: 0 AF XY: 0.000270 AC XY: 18AN XY: 66608
GnomAD4 exome AF: 0.000348 AC: 478AN: 1373394Hom.: 1 Cov.: 37 AF XY: 0.000338 AC XY: 229AN XY: 677576
GnomAD4 genome AF: 0.000302 AC: 46AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.979G>A (p.A327T) alteration is located in exon 2 (coding exon 2) of the SP8 gene. This alteration results from a G to A substitution at nucleotide position 979, causing the alanine (A) at amino acid position 327 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