X-105908827-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_198465.4(NRK):c.1186C>T(p.Pro396Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000091 in 1,208,434 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198465.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NRK | ENST00000243300.14 | c.1186C>T | p.Pro396Ser | missense_variant | Exon 13 of 29 | 1 | NM_198465.4 | ENSP00000434830.1 | ||
NRK | ENST00000428173.3 | n.*1181C>T | non_coding_transcript_exon_variant | Exon 13 of 23 | 2 | ENSP00000438378.2 | ||||
NRK | ENST00000428173.3 | n.*1181C>T | 3_prime_UTR_variant | Exon 13 of 23 | 2 | ENSP00000438378.2 |
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111577Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33755
GnomAD3 exomes AF: 0.00000553 AC: 1AN: 180769Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67053
GnomAD4 exome AF: 0.00000821 AC: 9AN: 1096857Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 4AN XY: 362335
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111577Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33755
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1186C>T (p.P396S) alteration is located in exon 13 (coding exon 13) of the NRK gene. This alteration results from a C to T substitution at nucleotide position 1186, causing the proline (P) at amino acid position 396 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