11-71450017-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000529369.2(DHCR7-DT):​n.324+1132A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,122 control chromosomes in the GnomAD database, including 28,437 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.59 ( 28437 hom., cov: 32)

Consequence

DHCR7-DT
ENST00000529369.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.66
Variant links:
Genes affected
DHCR7-DT (HGNC:56822): (DHCR7 divergent transcript)
DHCR7 (HGNC:2860): (7-dehydrocholesterol reductase) This gene encodes an enzyme that removes the C(7-8) double bond in the B ring of sterols and catalyzes the conversion of 7-dehydrocholesterol to cholesterol. This gene is ubiquitously expressed and its transmembrane protein localizes to the endoplasmic reticulum membrane and nuclear outer membrane. Mutations in this gene cause Smith-Lemli-Opitz syndrome (SLOS); a syndrome that is metabolically characterized by reduced serum cholesterol levels and elevated serum 7-dehydrocholesterol levels and phenotypically characterized by cognitive disability, facial dysmorphism, syndactyly of second and third toes, and holoprosencephaly in severe cases to minimal physical abnormalities and near-normal intelligence in mild cases. Alternative splicing results in multiple transcript variants that encode the same protein.[provided by RefSeq, Aug 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DHCR7-DTENST00000529369.2 linkuse as main transcriptn.324+1132A>G intron_variant, non_coding_transcript_variant 2
DHCR7ENST00000527452.1 linkuse as main transcriptc.-131-2283T>C intron_variant 4 ENSP00000436007

Frequencies

GnomAD3 genomes
AF:
0.588
AC:
89414
AN:
152004
Hom.:
28411
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.419
Gnomad AMI
AF:
0.688
Gnomad AMR
AF:
0.536
Gnomad ASJ
AF:
0.615
Gnomad EAS
AF:
0.380
Gnomad SAS
AF:
0.210
Gnomad FIN
AF:
0.583
Gnomad MID
AF:
0.456
Gnomad NFE
AF:
0.745
Gnomad OTH
AF:
0.565
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.588
AC:
89489
AN:
152122
Hom.:
28437
Cov.:
32
AF XY:
0.571
AC XY:
42478
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.420
Gnomad4 AMR
AF:
0.536
Gnomad4 ASJ
AF:
0.615
Gnomad4 EAS
AF:
0.381
Gnomad4 SAS
AF:
0.212
Gnomad4 FIN
AF:
0.583
Gnomad4 NFE
AF:
0.745
Gnomad4 OTH
AF:
0.558
Alfa
AF:
0.638
Hom.:
5395
Bravo
AF:
0.588
Asia WGS
AF:
0.288
AC:
1006
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.86
DANN
Benign
0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7928249; hg19: chr11-71161063; API