chr5-423975-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001377236.1(AHRR):c.706C>T(p.Leu236=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000438 in 1,598,550 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001377236.1 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AHRR | NM_001377236.1 | c.706C>T | p.Leu236= | splice_region_variant, synonymous_variant | 7/11 | ENST00000684583.1 | |
PDCD6-AHRR | NR_165159.2 | n.999C>T | splice_region_variant, non_coding_transcript_exon_variant | 9/14 | |||
AHRR | NM_001377239.1 | c.706C>T | p.Leu236= | splice_region_variant, synonymous_variant | 7/11 | ||
PDCD6-AHRR | NR_165163.2 | n.999C>T | splice_region_variant, non_coding_transcript_exon_variant | 9/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AHRR | ENST00000684583.1 | c.706C>T | p.Leu236= | splice_region_variant, synonymous_variant | 7/11 | NM_001377236.1 | P1 | ||
AHRR | ENST00000316418.10 | c.706C>T | p.Leu236= | splice_region_variant, synonymous_variant | 7/11 | 1 | P1 | ||
AHRR | ENST00000506456.1 | c.286C>T | p.Leu96= | splice_region_variant, synonymous_variant | 3/7 | 2 | |||
AHRR | ENST00000510910.1 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000422 AC: 1AN: 236912Hom.: 0 AF XY: 0.00000772 AC XY: 1AN XY: 129522
GnomAD4 exome AF: 0.00000346 AC: 5AN: 1446344Hom.: 0 Cov.: 33 AF XY: 0.00000278 AC XY: 2AN XY: 719744
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | AHRR: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at