rs10185319

Positions:

• chr2-241314580-C-A
• chr2-241314580-C-G
• chr2-241314580-C-T

Variant summary

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

The ENST00000310931.10(HDLBP):​c.-103+990G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 152,050 control chromosomes in the GnomAD database, including 48,887 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 0.80 (48887 hom., cov: 31)
• Consequence: HDLBP ENST00000310931.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HDLBP	NM_005336.6	c.-103+990G>T		intron_variant		ENST00000310931.10	NP_005327.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HDLBP	ENST00000310931.10	c.-103+990G>T		intron_variant		1	NM_005336.6	ENSP00000312042	P1

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121592 AN: 151932 Hom.: 48825 Cov.: 31

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.800 AC: 121714 AN: 152050 Hom.: 48887 Cov.: 31 AF XY: 0.804 AC XY: 59800 AN XY: 74336

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.947

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.825

Alfa AF: 0.802 Hom.: 62589

Bravo AF: 0.809

Asia WGS AF: 0.841 AC: 2925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.0
DANN	Benign	0.62

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: rs10185319; hg19: chr2-242253995;