rs187464517
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_020921.4(NIN):āc.3665A>Gā(p.Gln1222Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000137 in 1,613,990 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_020921.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NIN | NM_020921.4 | c.3665A>G | p.Gln1222Arg | missense_variant | 18/31 | ENST00000530997.7 | NP_065972.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NIN | ENST00000530997.7 | c.3665A>G | p.Gln1222Arg | missense_variant | 18/31 | 5 | NM_020921.4 | ENSP00000436092 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152186Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000697 AC: 175AN: 251030Hom.: 1 AF XY: 0.000575 AC XY: 78AN XY: 135738
GnomAD4 exome AF: 0.000139 AC: 203AN: 1461686Hom.: 1 Cov.: 64 AF XY: 0.000124 AC XY: 90AN XY: 727170
GnomAD4 genome AF: 0.000118 AC: 18AN: 152304Hom.: 0 Cov.: 31 AF XY: 0.000148 AC XY: 11AN XY: 74486
ClinVar
Submissions by phenotype
Seckel syndrome 7 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2012 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at