rs13394027

Variant names:

• chr2-20682296-G-A
• rs13394027
• XR_001738874.2:n.*193C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-20682296-G-A
• chr2-20682296-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001738874.2(LDAH):​n.*193C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,080 control chromosomes in the GnomAD database, including 3,425 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 0.19 (3425 hom., cov: 33)
• Consequence: LDAH XR_001738874.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 27 publications found

Genes affected

LDAH (HGNC:26145): (lipid droplet associated hydrolase) Predicted to enable lipase activity. Predicted to be involved in lipid storage. Predicted to be located in endoplasmic reticulum. Predicted to be active in lipid droplet. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LDAH	XR_001738874.2	n.*193C>T		downstream_gene_variant
LDAH	XR_007079563.1	n.*193C>T		downstream_gene_variant
LDAH	XR_007079565.1	n.*193C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28421 AN: 151962 Hom.: 3414 Cov.: 33

Gnomad AFR AF: 0.0468

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.187 AC: 28428 AN: 152080 Hom.: 3425 Cov.: 33 AF XY: 0.193 AC XY: 14321 AN XY: 74354

African (AFR) AF: 0.0466 AC: 1934 AN: 41508

American (AMR) AF: 0.222 AC: 3388 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3470

East Asian (EAS) AF: 0.454 AC: 2347 AN: 5166

South Asian (SAS) AF: 0.307 AC: 1482 AN: 4822

European-Finnish (FIN) AF: 0.255 AC: 2693 AN: 10552

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15143 AN: 67964

Other (OTH) AF: 0.224 AC: 473 AN: 2112

Alfa AF: 0.203 Hom.: 5216

Bravo AF: 0.175

Asia WGS AF: 0.376 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.10
DANN	Benign	0.89
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs13394027; hg19: chr2-20882056;