NM_001360.3:c.-131-61T>G

Variant names:

• chr11-71447795-A-C
• rs3750997
• NM_001360.3:c.-131-61T>G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001360.3(DHCR7):​c.-131-61T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 152,306 control chromosomes in the GnomAD database, including 27,997 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.58 (27938 hom., cov: 34)
  • Exomes 𝑓: 0.78 (59 hom.)
• Consequence: DHCR7 NM_001360.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.938
• Publications: 26 publications found

Genes affected

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]

DHCR7 Gene-Disease associations (from GenCC):

• Smith-Lemli-Opitz syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Myriad Women’s Health, Laboratory for Molecular Medicine, ClinGen, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 11-71447795-A-C is Benign according to our data. Variant chr11-71447795-A-C is described in ClinVar as Benign. ClinVar VariationId is 1290900.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DHCR7	NM_001360.3	MANE Select	c.-131-61T>G		intron	N/A	NP_001351.2
	DHCR7	NM_001425107.1		c.-131-61T>G		intron	N/A	NP_001412036.1
	DHCR7	NM_001425108.1		c.-131-61T>G		intron	N/A	NP_001412037.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DHCR7	ENST00000355527.8	TSL:1 MANE Select	c.-131-61T>G		intron	N/A	ENSP00000347717.4
	DHCR7	ENST00000407721.6	TSL:1	c.-131-61T>G		intron	N/A	ENSP00000384739.2
	DHCR7	ENST00000685320.1		c.-365-61T>G		intron	N/A	ENSP00000509319.1

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88731 AN: 151998 Hom.: 27908 Cov.: 34

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.557

GnomAD4 exome AF: 0.784 AC: 149 AN: 190 Hom.: 59 Cov.: 0 AF XY: 0.793 AC XY: 111 AN XY: 140

African (AFR) AF: 0.417 AC: 5 AN: 12

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 6 AN: 8

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.831 AC: 123 AN: 148

Other (OTH) AF: 0.786 AC: 11 AN: 14

GnomAD4 genome AF: 0.584 AC: 88806 AN: 152116 Hom.: 27938 Cov.: 34 AF XY: 0.569 AC XY: 42293 AN XY: 74352

African (AFR) AF: 0.407 AC: 16899 AN: 41510

American (AMR) AF: 0.561 AC: 8577 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2149 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2222 AN: 5168

South Asian (SAS) AF: 0.209 AC: 1009 AN: 4826

European-Finnish (FIN) AF: 0.568 AC: 6000 AN: 10568

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 50035 AN: 67980

Other (OTH) AF: 0.552 AC: 1164 AN: 2110

Alfa AF: 0.678 Hom.: 59066

Bravo AF: 0.585

Asia WGS AF: 0.309 AC: 1076 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

May 11, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.62
DANN	Benign	0.65
PhyloP100		-0.94
PromoterAI		-0.012	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3750997; hg19: chr11-71158841;