2-227240169-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_000091.5(COL4A3):c.171C>T(p.Pro57=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,610,960 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. P57P) has been classified as Likely benign.
Frequency
Consequence
NM_000091.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A3 | NM_000091.5 | c.171C>T | p.Pro57= | synonymous_variant | 3/52 | ENST00000396578.8 | |
MFF-DT | NR_102371.1 | n.1593-1995G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A3 | ENST00000396578.8 | c.171C>T | p.Pro57= | synonymous_variant | 3/52 | 1 | NM_000091.5 | P1 | |
MFF-DT | ENST00000439598.6 | n.1593-1995G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.000394 AC: 60AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000128 AC: 31AN: 242952Hom.: 0 AF XY: 0.0000911 AC XY: 12AN XY: 131762
GnomAD4 exome AF: 0.0000980 AC: 143AN: 1458686Hom.: 0 Cov.: 32 AF XY: 0.0000896 AC XY: 65AN XY: 725210
GnomAD4 genome AF: 0.000387 AC: 59AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74450
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 01, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Oct 31, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at