21-46191444-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_002340.6(LSS):c.2068-209T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,138 control chromosomes in the GnomAD database, including 2,676 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.17 (2676 hom., cov: 32)
• Consequence: LSS NM_002340.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.269

Genes affected

LSS (HGNC:6708): (lanosterol synthase) The protein encoded by this gene catalyzes the conversion of (S)-2,3 oxidosqualene to lanosterol. The encoded protein is a member of the terpene cyclase/mutase family and catalyzes the first step in the biosynthesis of cholesterol, steroid hormones, and vitamin D. Alternative splicing results in multiple transcript variants encoding different isoforms.[provided by RefSeq, Feb 2009]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 21-46191444-A-G is Benign according to our data. Variant chr21-46191444-A-G is described in ClinVar as [Benign]. Clinvar id is 1266874.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LSS	NM_002340.6	c.2068-209T>C		intron_variant		ENST00000397728.8
LSS	NM_001001438.3	c.2068-209T>C		intron_variant
LSS	NM_001145436.2	c.2035-209T>C		intron_variant
LSS	NM_001145437.2	c.1828-209T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LSS	ENST00000397728.8	c.2068-209T>C		intron_variant		1	NM_002340.6	P1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26525 AN: 152020 Hom.: 2674 Cov.: 32

Gnomad AFR AF: 0.0933

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.183

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.174 AC: 26540 AN: 152138 Hom.: 2676 Cov.: 32 AF XY: 0.175 AC XY: 12990 AN XY: 74356

Gnomad4 AFR AF: 0.0934

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.0278

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.185

Alfa AF: 0.106 Hom.: 175

Bravo AF: 0.162

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 03, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.2
Dann	Benign	0.69
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2187119; hg19: chr21-47611358;