11-57744573-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001145101.3(BTBD18):c.1700G>A(p.Gly567Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000516 in 1,551,652 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001145101.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BTBD18 | NM_001145101.3 | c.1700G>A | p.Gly567Glu | missense_variant | Exon 3 of 3 | ENST00000422652.6 | NP_001138573.1 | |
BTBD18 | XM_017018128.2 | c.1700G>A | p.Gly567Glu | missense_variant | Exon 3 of 3 | XP_016873617.1 | ||
BTBD18 | XM_047427405.1 | c.1700G>A | p.Gly567Glu | missense_variant | Exon 4 of 4 | XP_047283361.1 | ||
TMX2-CTNND1 | NR_037646.1 | n.346+6905C>T | intron_variant | Intron 2 of 20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BTBD18 | ENST00000422652.6 | c.1700G>A | p.Gly567Glu | missense_variant | Exon 3 of 3 | 4 | NM_001145101.3 | ENSP00000394472.1 | ||
ENSG00000254732 | ENST00000531074.1 | n.*152+1589C>T | intron_variant | Intron 2 of 3 | 3 | ENSP00000457993.1 | ||||
ENSG00000288534 | ENST00000674060.1 | n.103+6905C>T | intron_variant | Intron 2 of 19 | ENSP00000501055.2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152138Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000429 AC: 6AN: 1399396Hom.: 0 Cov.: 34 AF XY: 0.00000435 AC XY: 3AN XY: 690206
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74462
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at