2-230873516-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030926.6(ITM2C):c.220T>A(p.Phe74Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000869 in 1,610,864 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_030926.6 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: 0.0000197 AC: 3AN: 152224Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 247718Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134112
GnomAD4 exome AF: 0.00000754 AC: 11AN: 1458640Hom.: 0 Cov.: 36 AF XY: 0.00000827 AC XY: 6AN XY: 725608
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152224Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.220T>A (p.F74I) alteration is located in exon 2 (coding exon 2) of the ITM2C gene. This alteration results from a T to A substitution at nucleotide position 220, causing the phenylalanine (F) at amino acid position 74 to be replaced by an isoleucine (I). 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