NM_001122955.4:c.346_347dupTT
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_001122955.4(BSCL2):c.346_347dupTT(p.Tyr117SerfsTer40) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,770 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (no stars). Synonymous variant affecting the same amino acid position (i.e. F116F) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001122955.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BSCL2 | NM_001122955.4 | c.346_347dupTT | p.Tyr117SerfsTer40 | frameshift_variant | Exon 2 of 11 | ENST00000360796.10 | NP_001116427.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BSCL2 | ENST00000360796.10 | c.346_347dupTT | p.Tyr117SerfsTer40 | frameshift_variant | Exon 2 of 11 | 1 | NM_001122955.4 | ENSP00000354032.5 | ||
HNRNPUL2-BSCL2 | ENST00000403734.2 | n.*397_*398dupTT | non_coding_transcript_exon_variant | Exon 15 of 24 | 2 | ENSP00000456010.1 | ||||
HNRNPUL2-BSCL2 | ENST00000403734.2 | n.*397_*398dupTT | 3_prime_UTR_variant | Exon 15 of 24 | 2 | ENSP00000456010.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250834Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135632
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461770Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727166
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Berardinelli-Seip congenital lipodystrophy Uncertain:1
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Congenital generalized lipodystrophy type 2 Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at