NM_019080.3:c.388C>T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019080.3(NDFIP2):c.388C>T(p.Pro130Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00029 in 1,613,900 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_019080.3 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 |
---|---|---|---|---|---|---|---|---|
NDFIP2 | NM_019080.3 | c.388C>T | p.Pro130Ser | missense_variant | Exon 2 of 8 | ENST00000218652.12 | NP_061953.2 | |
NDFIP2 | NM_001394685.1 | c.385C>T | p.Pro129Ser | missense_variant | Exon 2 of 8 | NP_001381614.1 | ||
NDFIP2 | NM_001161407.2 | c.388C>T | p.Pro130Ser | missense_variant | Exon 2 of 8 | NP_001154879.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251318Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135818
GnomAD4 exome AF: 0.000308 AC: 450AN: 1461700Hom.: 0 Cov.: 30 AF XY: 0.000271 AC XY: 197AN XY: 727154
GnomAD4 genome AF: 0.000118 AC: 18AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.388C>T (p.P130S) alteration is located in exon 2 (coding exon 2) of the NDFIP2 gene. This alteration results from a C to T substitution at nucleotide position 388, causing the proline (P) at amino acid position 130 to be replaced by a serine (S). 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