rs269951
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001127255.2(NLRP7):c.2682T>C(p.Tyr894Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 1,610,306 control chromosomes in the GnomAD database, including 255,126 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001127255.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLRP7 | NM_001127255.2 | c.2682T>C | p.Tyr894Tyr | synonymous_variant | Exon 9 of 11 | NP_001120727.1 | ||
NLRP7 | NM_001405531.1 | c.2682T>C | p.Tyr894Tyr | synonymous_variant | Exon 11 of 13 | NP_001392460.1 | ||
NLRP7 | NM_139176.4 | c.2598T>C | p.Tyr866Tyr | synonymous_variant | Exon 9 of 11 | NP_631915.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.554 AC: 84139AN: 151824Hom.: 23559 Cov.: 31
GnomAD3 exomes AF: 0.588 AC: 147809AN: 251440Hom.: 44097 AF XY: 0.589 AC XY: 80048AN XY: 135896
GnomAD4 exome AF: 0.561 AC: 818657AN: 1458364Hom.: 231546 Cov.: 34 AF XY: 0.565 AC XY: 409847AN XY: 725660
GnomAD4 genome AF: 0.554 AC: 84203AN: 151942Hom.: 23580 Cov.: 31 AF XY: 0.557 AC XY: 41388AN XY: 74254
ClinVar
Submissions by phenotype
Hydatidiform mole, recurrent, 1 Benign:3
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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. -
not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
Hydatidiform mole Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at