rs15129

Positions:

• chr2-241229561-T-C

Variant summary

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

The NM_005336.6(HDLBP):​c.*40A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 1,471,092 control chromosomes in the GnomAD database, including 49,240 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 0.24 (5488 hom., cov: 32)
  • Exomes 𝑓: 0.23 (43752 hom.)
• Consequence: HDLBP NM_005336.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

Genes affected

HDLBP (HGNC:4857): (high density lipoprotein binding protein) The protein encoded by this gene binds high density lipoprotein (HDL) and may function to regulate excess cholesterol levels in cells. The encoded protein also binds RNA and can induce heterochromatin formation. [provided by RefSeq, Mar 2016]

ANO7 (HGNC:31677): (anoctamin 7) This prostate-specific gene encodes a cytoplasmic protein, as well as a polytopic membrane protein which may serve as a target in prostate cancer diagnosis and immunotherapy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -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 = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HDLBP	NM_005336.6	c.*40A>G		3_prime_UTR_variant	28/28	ENST00000310931.10	NP_005327.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HDLBP	ENST00000310931	c.*40A>G		3_prime_UTR_variant	28/28	1	NM_005336.6	ENSP00000312042.4

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36372 AN: 151928 Hom.: 5461 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.232

GnomAD3 exomes AF: 0.305 AC: 73346 AN: 240312 Hom.: 14768 AF XY: 0.296 AC XY: 38653 AN XY: 130474

Gnomad AFR exome AF: 0.195

Gnomad AMR exome AF: 0.472

Gnomad ASJ exome AF: 0.163

Gnomad EAS exome AF: 0.758

Gnomad SAS exome AF: 0.341

Gnomad FIN exome AF: 0.345

Gnomad NFE exome AF: 0.191

Gnomad OTH exome AF: 0.266

GnomAD4 exome AF: 0.230 AC: 303044 AN: 1319046 Hom.: 43752 Cov.: 18 AF XY: 0.230 AC XY: 152741 AN XY: 663038

Gnomad4 AFR exome AF: 0.190

Gnomad4 AMR exome AF: 0.462

Gnomad4 ASJ exome AF: 0.167

Gnomad4 EAS exome AF: 0.720

Gnomad4 SAS exome AF: 0.337

Gnomad4 FIN exome AF: 0.336

Gnomad4 NFE exome AF: 0.189

Gnomad4 OTH exome AF: 0.235

GnomAD4 genome AF: 0.240 AC: 36439 AN: 152046 Hom.: 5488 Cov.: 32 AF XY: 0.252 AC XY: 18717 AN XY: 74322

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.237

Alfa AF: 0.202 Hom.: 3939

Bravo AF: 0.241

Asia WGS AF: 0.528 AC: 1833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
DANN	Benign	0.46
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs15129; hg19: chr2-242168976; COSMIC: COSV51471860; COSMIC: COSV51471860;