1-66801064-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005478.6(INSL5):c.158T>A(p.Ile53Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000329 in 1,611,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005478.6 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: 0.0000920 AC: 14AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000959 AC: 24AN: 250196Hom.: 0 AF XY: 0.0000813 AC XY: 11AN XY: 135220
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1459730Hom.: 0 Cov.: 28 AF XY: 0.0000275 AC XY: 20AN XY: 726146
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.158T>A (p.I53N) alteration is located in exon 1 (coding exon 1) of the INSL5 gene. This alteration results from a T to A substitution at nucleotide position 158, causing the isoleucine (I) at amino acid position 53 to be replaced by an asparagine (N). 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