rs6724257

Positions:

• chr2-241282982-A-G
• chr2-241282982-A-T

Variant summary

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

The NM_005336.6(HDLBP):​c.-102-14441T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,138 control chromosomes in the GnomAD database, including 8,592 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 0.32 (8592 hom., cov: 33)
• Consequence: HDLBP NM_005336.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

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]

HDLBP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HDLBP	NM_005336.6	c.-102-14441T>C		intron_variant		ENST00000310931.10	NP_005327.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HDLBP	ENST00000310931.10	c.-102-14441T>C		intron_variant		1	NM_005336.6	ENSP00000312042.4

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48956 AN: 152020 Hom.: 8584 Cov.: 33

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.322 AC: 48981 AN: 152138 Hom.: 8592 Cov.: 33 AF XY: 0.326 AC XY: 24238 AN XY: 74366

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.322

Alfa AF: 0.374 Hom.: 6348

Bravo AF: 0.304

Asia WGS AF: 0.462 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.71

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: rs6724257; hg19: chr2-242222397;