chr16-67431290-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_ModerateBP6_ModerateBP7BS1
The NM_000196.4(HSD11B2):c.42C>G(p.Leu14=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,266,788 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 Benign (★). Synonymous variant affecting the same amino acid position (i.e. L14L) has been classified as Likely benign.
Frequency
Consequence
NM_000196.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSD11B2 | NM_000196.4 | c.42C>G | p.Leu14= | synonymous_variant | 1/5 | ENST00000326152.6 | |
HSD11B2 | XM_047434048.1 | c.-48+511C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSD11B2 | ENST00000326152.6 | c.42C>G | p.Leu14= | synonymous_variant | 1/5 | 1 | NM_000196.4 | P1 | |
ENST00000567261.1 | n.135+40G>C | intron_variant, non_coding_transcript_variant | 3 | ||||||
HSD11B2 | ENST00000567684.2 | n.128+511C>G | intron_variant, non_coding_transcript_variant | 3 | |||||
HSD11B2 | ENST00000569303.1 | n.27+142C>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000665 AC: 10AN: 150480Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000361 AC: 2AN: 55442Hom.: 0 AF XY: 0.0000308 AC XY: 1AN XY: 32464
GnomAD4 exome AF: 0.0000143 AC: 16AN: 1116200Hom.: 0 Cov.: 30 AF XY: 0.0000111 AC XY: 6AN XY: 542528
GnomAD4 genome ? AF: 0.0000664 AC: 10AN: 150588Hom.: 0 Cov.: 31 AF XY: 0.0000952 AC XY: 7AN XY: 73560
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at