rs11680329

chr2-241247422-C-T

Variant summary

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

The NM_005336.6(HDLBP):c.1732-280G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 458,524 control chromosomes in the GnomAD database, including 6,740 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 0.14 (1962 hom., cov: 32)
  • Exomes 𝑓: 0.16 (4778 hom.)
• Consequence: HDLBP NM_005336.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HDLBP	NM_005336.6	c.1732-280G>A		intron_variant		ENST00000310931.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HDLBP	ENST00000310931.10	c.1732-280G>A		intron_variant		1	NM_005336.6	P1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21338 AN: 152110 Hom.: 1963 Cov.: 32

Gnomad AFR AF: 0.0398

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0520

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.157

GnomAD4 exome AF: 0.159 AC: 48690 AN: 306296 Hom.: 4778 Cov.: 0 AF XY: 0.153 AC XY: 25003 AN XY: 163748

Gnomad4 AFR exome AF: 0.0388

Gnomad4 AMR exome AF: 0.118

Gnomad4 ASJ exome AF: 0.205

Gnomad4 EAS exome AF: 0.000276

Gnomad4 SAS exome AF: 0.0573

Gnomad4 FIN exome AF: 0.164

Gnomad4 NFE exome AF: 0.204

Gnomad4 OTH exome AF: 0.159

GnomAD4 genome AF: 0.140 AC: 21325 AN: 152228 Hom.: 1962 Cov.: 32 AF XY: 0.139 AC XY: 10342 AN XY: 74440

Gnomad4 AFR AF: 0.0396

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0512

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.155

Alfa AF: 0.175 Hom.: 824

Bravo AF: 0.135

Asia WGS AF: 0.0290 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.36
Dann	Benign	0.51

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: rs11680329; hg19: chr2-242186837;