19-55014324-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001083899.2(GP6):c.1621C>T(p.Leu541=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000766 in 1,592,180 control chromosomes in the GnomAD database, including 1 homozygotes. 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. L541L) has been classified as Likely benign.
Frequency
Consequence
NM_001083899.2 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 |
---|---|---|---|---|---|---|---|
GP6 | NM_001083899.2 | c.1621C>T | p.Leu541= | synonymous_variant | 8/8 | ENST00000310373.7 | |
GP6-AS1 | XR_001754012.3 | n.121+7860G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GP6 | ENST00000310373.7 | c.1621C>T | p.Leu541= | synonymous_variant | 8/8 | 1 | NM_001083899.2 | ||
GP6-AS1 | ENST00000593060.5 | n.155+7860G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000250 AC: 38AN: 152122Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000175 AC: 43AN: 245952Hom.: 1 AF XY: 0.000112 AC XY: 15AN XY: 133630
GnomAD4 exome AF: 0.0000569 AC: 82AN: 1439940Hom.: 1 Cov.: 29 AF XY: 0.0000432 AC XY: 31AN XY: 717772
GnomAD4 genome ? AF: 0.000263 AC: 40AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74432
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at