Genetic Variant HILPDA:c.-267C>G (chr7-128455825-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.852

Publications

2 publications found

Variant links:

COSMIC-nc: COSV57556118

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]

HILPDA links:

ENSG00000273184 (HGNC:):

ENSG00000273184 links:

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

HILPDA-AS1 links:

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

EFCAB3P1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 link	c.-267C>G		upstream_gene_variant		ENST00000257696.5	NP_037464.1	Q9Y5L2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HILPDA	ENST00000257696.5 link	c.-267C>G		upstream_gene_variant		1	NM_013332.4	ENSP00000257696.4		Q9Y5L2

Frequencies

GnomAD3 genomes

AF:

0.0643

AC:

9777

AN:

152154

Hom.:

567

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.0681

AC:

9096

AN:

133494

AF XY:

0.0711

show subpopulations

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 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.:

AF XY:

0.0640

AC XY:

11050

AN XY:

172600

show subpopulations

African (AFR)

AF:

0.118

AC:

1006

AN:

8554

American (AMR)

AF:

0.0339

AC:

924

AN:

27234

Ashkenazi Jewish (ASJ)

AF:

0.0590

AC:

632

AN:

10714

East Asian (EAS)

AF:

0.226

AC:

2070

AN:

9168

South Asian (SAS)

AF:

0.131

AC:

7807

AN:

59562

European-Finnish (FIN)

AF:

0.00660

AC:

AN:

12720

Middle Eastern (MID)

AF:

0.0679

AC:

162

AN:

2386

European-Non Finnish (NFE)

AF:

0.0250

AC:

3973

AN:

158610

Other (OTH)

AF:

0.0548

AC:

776

AN:

14170

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

853

1707

2560

3414

4267

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

224

336

448

560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0643

AC:

9784

AN:

152270

Hom.:

566

Cov.:

AF XY:

0.0652

AC XY:

4857

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.121

AC:

5041

AN:

41548

American (AMR)

AF:

0.0435

AC:

665

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0613

AC:

213

AN:

3472

East Asian (EAS)

AF:

0.226

AC:

1168

AN:

5168

South Asian (SAS)

AF:

0.138

AC:

666

AN:

4828

European-Finnish (FIN)

AF:

0.00461

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.0651

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0269

AC:

1828

AN:

68018

Other (OTH)

AF:

0.0626

AC:

132

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

443

886

1328

1771

2214

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0219

Hom.:

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

(source)

DANN

Benign

0.75

PhyloP100

-0.85

PromoterAI

0.059

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over