chr10-89213735-G-A

Variant names:

• chr10-89213735-G-A
• rs13500
• NM_000235.4:c.*1093C>T

Variant summary

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

The NM_000235.4(LIPA):​c.*1093C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,176 control chromosomes in the GnomAD database, including 1,130 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.11 (1130 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LIPA NM_000235.4 3_prime_UTR
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -1.04
• Publications: 16 publications found

Genes affected

LIPA (HGNC:6617): (lipase A, lysosomal acid type) This gene encodes lipase A, the lysosomal acid lipase (also known as cholesterol ester hydrolase). This enzyme functions in the lysosome to catalyze the hydrolysis of cholesteryl esters and triglycerides. Mutations in this gene can result in Wolman disease and cholesteryl ester storage disease. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2014]

LIPA Gene-Disease associations (from GenCC):

• lysosomal acid lipase deficiency

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• lysosomal acid lipase deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Myriad Women’s Health, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• cholesteryl ester storage disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Wolman disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 10-89213735-G-A is Benign according to our data. Variant chr10-89213735-G-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 301549.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000235.4. 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
	LIPA	NM_000235.4	MANE Select	c.*1093C>T		3_prime_UTR	Exon 10 of 10	NP_000226.2	P38571-1
	LIPA	NM_001440836.1		c.*1093C>T		3_prime_UTR	Exon 11 of 11	NP_001427765.1
	LIPA	NM_001440837.1		c.*1093C>T		3_prime_UTR	Exon 10 of 10	NP_001427766.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPA	ENST00000336233.10	TSL:1 MANE Select	c.*1093C>T		3_prime_UTR	Exon 10 of 10	ENSP00000337354.5	P38571-1
	LIPA	ENST00000868683.1		c.*1093C>T		3_prime_UTR	Exon 10 of 10	ENSP00000538742.1
	LIPA	ENST00000938131.1		c.*1093C>T		3_prime_UTR	Exon 10 of 10	ENSP00000608190.1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16788 AN: 152058 Hom.: 1128 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0756

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0891

Gnomad FIN AF: 0.0362

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0996

Gnomad OTH AF: 0.115

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.110 AC: 16803 AN: 152176 Hom.: 1130 Cov.: 32 AF XY: 0.107 AC XY: 7926 AN XY: 74414

African (AFR) AF: 0.172 AC: 7119 AN: 41496

American (AMR) AF: 0.0755 AC: 1153 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 525 AN: 3470

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5190

South Asian (SAS) AF: 0.0898 AC: 433 AN: 4822

European-Finnish (FIN) AF: 0.0362 AC: 384 AN: 10598

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0997 AC: 6777 AN: 68004

Other (OTH) AF: 0.113 AC: 239 AN: 2112

Alfa AF: 0.110 Hom.: 406

Bravo AF: 0.115

Asia WGS AF: 0.0520 AC: 182 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign/Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)
-	-	1	Lysosomal acid lipase deficiency (1)
-	-	1	Wolman disease (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.52
DANN	Benign	0.41
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13500; hg19: chr10-90973492;