17-63910511-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022579.3(CSHL1):āc.215A>Cā(p.Lys72Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000221 in 1,614,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_022579.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251492Hom.: 0 AF XY: 0.0000956 AC XY: 13AN XY: 135918
GnomAD4 exome AF: 0.000236 AC: 345AN: 1461890Hom.: 0 Cov.: 84 AF XY: 0.000239 AC XY: 174AN XY: 727246
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.215A>C (p.K72T) alteration is located in exon 3 (coding exon 3) of the CSHL1 gene. This alteration results from a A to C substitution at nucleotide position 215, causing the lysine (K) at amino acid position 72 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