1-1312287-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_017871.6(INTS11):c.1546C>T(p.His516Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00000358 in 1,398,212 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017871.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000128 AC: 2AN: 156508Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 82698
GnomAD4 exome AF: 0.00000358 AC: 5AN: 1398212Hom.: 0 Cov.: 36 AF XY: 0.00000290 AC XY: 2AN XY: 689708
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1546C>T (p.H516Y) alteration is located in exon 15 (coding exon 15) of the CPSF3L gene. This alteration results from a C to T substitution at nucleotide position 1546, causing the histidine (H) at amino acid position 516 to be replaced by a tyrosine (Y). 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