17-15978063-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001042697.2(ZSWIM7):c.407A>T(p.Lys136Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,700 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001042697.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZSWIM7 | NM_001042697.2 | c.407A>T | p.Lys136Met | missense_variant | Exon 5 of 5 | ENST00000399277.6 | NP_001036162.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152242Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249472Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135356
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461340Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727008
GnomAD4 genome AF: 0.000112 AC: 17AN: 152360Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74510
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.407A>T (p.K136M) alteration is located in exon 5 (coding exon 5) of the ZSWIM7 gene. This alteration results from a A to T substitution at nucleotide position 407, causing the lysine (K) at amino acid position 136 to be replaced by a methionine (M). 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