rs764300734
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004646.4(NPHS1):c.216C>T(p.Gly72=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,458 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. G72G) has been classified as Likely benign.
Frequency
Consequence
NM_004646.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPHS1 | NM_004646.4 | c.216C>T | p.Gly72= | synonymous_variant | 2/29 | ENST00000378910.10 | |
KIRREL2 | XM_011527362.2 | c.-392G>A | 5_prime_UTR_variant | 1/16 | |||
KIRREL2 | XM_011527363.2 | c.-383G>A | 5_prime_UTR_variant | 1/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPHS1 | ENST00000378910.10 | c.216C>T | p.Gly72= | synonymous_variant | 2/29 | 1 | NM_004646.4 | P2 | |
NPHS1 | ENST00000353632.6 | c.216C>T | p.Gly72= | synonymous_variant | 2/28 | 5 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000408 AC: 1AN: 245244Hom.: 0 AF XY: 0.00000748 AC XY: 1AN XY: 133716
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461458Hom.: 0 Cov.: 35 AF XY: 0.00000550 AC XY: 4AN XY: 727034
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 05, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at