2-20820030-C-T

Variant names:

• chr2-20820030-C-T
• rs1098152
• NM_021925.4:c.-3+3007G>A

Variant summary

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

The NM_021925.4(LDAH):​c.-3+3007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 149,944 control chromosomes in the GnomAD database, including 4,350 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 0.15 (4350 hom., cov: 31)
• Consequence: LDAH NM_021925.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LDAH	NM_021925.4	c.-3+3007G>A		intron_variant	Intron 1 of 6	ENST00000237822.8	NP_068744.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LDAH	ENST00000237822.8	c.-3+3007G>A		intron_variant	Intron 1 of 6	1	NM_021925.4	ENSP00000237822.3

Frequencies

GnomAD3 genomes AF: 0.152 AC: 22712 AN: 149838 Hom.: 4331 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.0945

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0359

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0318

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.152 AC: 22774 AN: 149944 Hom.: 4350 Cov.: 31 AF XY: 0.147 AC XY: 10789 AN XY: 73288

African (AFR) AF: 0.459 AC: 18292 AN: 39866

American (AMR) AF: 0.0947 AC: 1432 AN: 15114

Ashkenazi Jewish (ASJ) AF: 0.0228 AC: 79 AN: 3460

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5168

South Asian (SAS) AF: 0.0259 AC: 124 AN: 4780

European-Finnish (FIN) AF: 0.0359 AC: 377 AN: 10510

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.0319 AC: 2158 AN: 67754

Other (OTH) AF: 0.124 AC: 259 AN: 2090

Alfa AF: 0.0329 Hom.: 59

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.66
PhyloP100		-1.4
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: rs1098152; hg19: chr2-21019790;