rs567600444
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 4P and 8B. PM1PM5BP4_StrongBS2
The NM_001360.3(DHCR7):c.1091C>T(p.Thr364Met) variant causes a missense change. The variant allele was found at a frequency of 0.00016 in 1,613,132 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T364A) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001360.3 missense
Scores
Clinical Significance
Conservation
Publications
- Smith-Lemli-Opitz syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Myriad Women’s Health, ClinGen, Orphanet, Laboratory for Molecular Medicine
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001360.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DHCR7 | MANE Select | c.1091C>T | p.Thr364Met | missense | Exon 9 of 9 | NP_001351.2 | A0A024R5F7 | ||
| DHCR7 | c.1142C>T | p.Thr381Met | missense | Exon 10 of 10 | NP_001412036.1 | A0A804HI25 | |||
| DHCR7 | c.1127C>T | p.Thr376Met | missense | Exon 9 of 9 | NP_001412037.1 | A0A804HJQ7 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DHCR7 | TSL:1 MANE Select | c.1091C>T | p.Thr364Met | missense | Exon 9 of 9 | ENSP00000347717.4 | Q9UBM7 | ||
| DHCR7 | TSL:1 | c.1091C>T | p.Thr364Met | missense | Exon 9 of 9 | ENSP00000384739.2 | Q9UBM7 | ||
| DHCR7 | c.506C>T | p.Thr169Met | missense | Exon 8 of 8 | ENSP00000509319.1 | B4E1K5 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152250Hom.: 0 Cov.: 34 show subpopulations
GnomAD2 exomes AF: 0.000346 AC: 86AN: 248776 AF XY: 0.000489 show subpopulations
GnomAD4 exome AF: 0.000164 AC: 239AN: 1460764Hom.: 3 Cov.: 37 AF XY: 0.000256 AC XY: 186AN XY: 726702 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000125 AC: 19AN: 152368Hom.: 0 Cov.: 34 AF XY: 0.000148 AC XY: 11AN XY: 74512 show subpopulations
Age Distribution
ClinVar
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at