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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;