6-75923668-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001563.4(IMPG1):c.2282G>A(p.Ser761Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 1,582,566 control chromosomes in the GnomAD database, including 47,346 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Synonymous variant affecting the same amino acid position (i.e. S761S) has been classified as Likely benign.
Frequency
Consequence
NM_001563.4 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IMPG1 | NM_001563.4 | c.2282G>A | p.Ser761Asn | missense_variant | 16/17 | ENST00000369950.8 | |
IMPG1 | NM_001282368.2 | c.2048G>A | p.Ser683Asn | missense_variant | 15/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IMPG1 | ENST00000369950.8 | c.2282G>A | p.Ser761Asn | missense_variant | 16/17 | 1 | NM_001563.4 | P2 | |
IMPG1 | ENST00000611179.4 | c.2048G>A | p.Ser683Asn | missense_variant | 15/16 | 5 | A2 | ||
IMPG1 | ENST00000369952.3 | c.365G>A | p.Ser122Asn | missense_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.185 AC: 28037AN: 151950Hom.: 3222 Cov.: 32
GnomAD3 exomes AF: 0.191 AC: 46441AN: 243518Hom.: 5029 AF XY: 0.194 AC XY: 25518AN XY: 131524
GnomAD4 exome AF: 0.239 AC: 342209AN: 1430498Hom.: 44121 Cov.: 26 AF XY: 0.238 AC XY: 169443AN XY: 712744
GnomAD4 genome AF: 0.184 AC: 28045AN: 152068Hom.: 3225 Cov.: 32 AF XY: 0.180 AC XY: 13348AN XY: 74350
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Retinal dystrophy Benign:1
Benign, criteria provided, single submitter | research | Dept Of Ophthalmology, Nagoya University | Oct 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at