6-139242885-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153235.4(TXLNB):c.1696G>A(p.Glu566Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000694 in 1,614,096 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153235.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000143 AC: 36AN: 251144Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135780
GnomAD4 exome AF: 0.0000746 AC: 109AN: 1461846Hom.: 1 Cov.: 35 AF XY: 0.0000935 AC XY: 68AN XY: 727222
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74428
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1696G>A (p.E566K) alteration is located in exon 10 (coding exon 9) of the TXLNB gene. This alteration results from a G to A substitution at nucleotide position 1696, causing the glutamic acid (E) at amino acid position 566 to be replaced by a lysine (K). 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