rs3747992
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_015102.5(NPHP4):c.2802C>T(p.Arg934Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 1,575,438 control chromosomes in the GnomAD database, including 129,927 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_015102.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPHP4 | NM_015102.5 | c.2802C>T | p.Arg934Arg | synonymous_variant | Exon 20 of 30 | ENST00000378156.9 | NP_055917.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPHP4 | ENST00000378156.9 | c.2802C>T | p.Arg934Arg | synonymous_variant | Exon 20 of 30 | 1 | NM_015102.5 | ENSP00000367398.4 | ||
NPHP4 | ENST00000378169.7 | n.*1703C>T | non_coding_transcript_exon_variant | Exon 17 of 27 | 1 | ENSP00000367411.3 | ||||
NPHP4 | ENST00000489180.6 | n.*350C>T | non_coding_transcript_exon_variant | Exon 21 of 33 | 2 | ENSP00000423747.1 | ||||
NPHP4 | ENST00000378169.7 | n.*1703C>T | 3_prime_UTR_variant | Exon 17 of 27 | 1 | ENSP00000367411.3 | ||||
NPHP4 | ENST00000489180.6 | n.*350C>T | 3_prime_UTR_variant | Exon 21 of 33 | 2 | ENSP00000423747.1 |
Frequencies
GnomAD3 genomes AF: 0.378 AC: 57511AN: 151998Hom.: 11520 Cov.: 34
GnomAD3 exomes AF: 0.431 AC: 100525AN: 233474Hom.: 22969 AF XY: 0.428 AC XY: 54378AN XY: 127034
GnomAD4 exome AF: 0.402 AC: 572042AN: 1423322Hom.: 118404 Cov.: 35 AF XY: 0.402 AC XY: 282278AN XY: 701630
GnomAD4 genome AF: 0.378 AC: 57535AN: 152116Hom.: 11523 Cov.: 34 AF XY: 0.382 AC XY: 28381AN XY: 74354
ClinVar
Submissions by phenotype
not specified Benign:5
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not provided Benign:2
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Nephronophthisis 4 Benign:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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Senior-Loken syndrome 4 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Nephronophthisis Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at