rs12721613
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003889.4(NR1I2):c.79C>T(p.Pro27Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00696 in 1,614,172 control chromosomes in the GnomAD database, including 615 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003889.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NR1I2 | NM_003889.4 | c.79C>T | p.Pro27Ser | missense_variant | 2/9 | ENST00000393716.8 | NP_003880.3 | |
NR1I2 | NM_022002.3 | c.196C>T | p.Pro66Ser | missense_variant | 2/9 | NP_071285.1 | ||
NR1I2 | NM_033013.3 | c.79C>T | p.Pro27Ser | missense_variant | 2/9 | NP_148934.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NR1I2 | ENST00000393716.8 | c.79C>T | p.Pro27Ser | missense_variant | 2/9 | 1 | NM_003889.4 | ENSP00000377319.3 | ||
ENSG00000285585 | ENST00000648112.1 | c.*102C>T | 3_prime_UTR_variant | 18/18 | ENSP00000497876.1 |
Frequencies
GnomAD3 genomes AF: 0.0357 AC: 5425AN: 152170Hom.: 326 Cov.: 32
GnomAD3 exomes AF: 0.00980 AC: 2465AN: 251492Hom.: 128 AF XY: 0.00715 AC XY: 972AN XY: 135922
GnomAD4 exome AF: 0.00397 AC: 5799AN: 1461884Hom.: 290 Cov.: 32 AF XY: 0.00347 AC XY: 2526AN XY: 727242
GnomAD4 genome AF: 0.0357 AC: 5430AN: 152288Hom.: 325 Cov.: 32 AF XY: 0.0334 AC XY: 2490AN XY: 74474
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at