2-20763879-T-A

Position:

• chr2-20763879-T-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_021925.4(LDAH):​c.468+10931A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,218 control chromosomes in the GnomAD database, including 2,739 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 0.17 (2739 hom., cov: 33)
• Consequence: LDAH NM_021925.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.35

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]

LDAH (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LDAH	NM_021925.4	c.468+10931A>T		intron_variant		ENST00000237822.8	NP_068744.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LDAH	ENST00000237822.8	c.468+10931A>T		intron_variant		1	NM_021925.4	ENSP00000237822.3

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26140 AN: 152102 Hom.: 2736 Cov.: 33

Gnomad AFR AF: 0.0581

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.172 AC: 26150 AN: 152218 Hom.: 2739 Cov.: 33 AF XY: 0.174 AC XY: 12929 AN XY: 74392

Gnomad4 AFR AF: 0.0580

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.151

Alfa AF: 0.0966 Hom.: 144

Bravo AF: 0.172

Asia WGS AF: 0.193 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	18
DANN	Benign	0.82

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: rs17665125; hg19: chr2-20963639;