rs2288555

Variant names:

• chr7-128455825-C-G
• rs2288555
• NM_013332.4:c.-267C>G

Your query was ambiguous. Multiple possible variants found:

• chr7-128455825-C-G
• chr7-128455825-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013332.4(HILPDA):​c.-267C>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0598 in 455,388 control chromosomes in the GnomAD database, including 1,581 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 0.064 (566 hom., cov: 33)
  • Exomes 𝑓: 0.058 (1015 hom.)
• Consequence: HILPDA NM_013332.4 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852

Genes affected

HILPDA (HGNC:28859): (hypoxia inducible lipid droplet associated) Enables signaling receptor binding activity. Involved in several processes, including autocrine signaling; cellular response to hypoxia; and positive regulation of lipid storage. Located in several cellular components, including cell surface; lipid droplet; and secretory granule. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000273184 (HGNC:):

HILPDA-AS1 (HGNC:55641): (HILPDA antisense RNA 1)

EFCAB3P1 (HGNC:56232): (EFCAB3 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HILPDA	NM_013332.4	c.-267C>G		upstream_gene_variant		ENST00000257696.5	NP_037464.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HILPDA	ENST00000257696.5	c.-267C>G		upstream_gene_variant		1	NM_013332.4	ENSP00000257696.4

Frequencies

GnomAD3 genomes AF: 0.0643 AC: 9777 AN: 152154 Hom.: 567 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0435

Gnomad ASJ AF: 0.0613

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.00461

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0269

Gnomad OTH AF: 0.0618

GnomAD3 exomes AF: 0.0681 AC: 9096 AN: 133494 Hom.: 601 AF XY: 0.0711 AC XY: 5168 AN XY: 72644

Gnomad AFR exome AF: 0.119

Gnomad AMR exome AF: 0.0334

Gnomad ASJ exome AF: 0.0589

Gnomad EAS exome AF: 0.230

Gnomad SAS exome AF: 0.133

Gnomad FIN exome AF: 0.00549

Gnomad NFE exome AF: 0.0268

Gnomad OTH exome AF: 0.0555

GnomAD4 exome AF: 0.0575 AC: 17434 AN: 303118 Hom.: 1015 Cov.: 0 AF XY: 0.0640 AC XY: 11050 AN XY: 172600

Gnomad4 AFR exome AF: 0.118

Gnomad4 AMR exome AF: 0.0339

Gnomad4 ASJ exome AF: 0.0590

Gnomad4 EAS exome AF: 0.226

Gnomad4 SAS exome AF: 0.131

Gnomad4 FIN exome AF: 0.00660

Gnomad4 NFE exome AF: 0.0250

Gnomad4 OTH exome AF: 0.0548

GnomAD4 genome AF: 0.0643 AC: 9784 AN: 152270 Hom.: 566 Cov.: 33 AF XY: 0.0652 AC XY: 4857 AN XY: 74446

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.0435

Gnomad4 ASJ AF: 0.0613

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.00461

Gnomad4 NFE AF: 0.0269

Gnomad4 OTH AF: 0.0626

Alfa AF: 0.0219 Hom.: 17

Bravo AF: 0.0682

Asia WGS AF: 0.171 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.2
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2288555; hg19: chr7-128095879; COSMIC: COSV57556118;