rs6752050

Variant names:

• chr2-241289365-T-C
• rs6752050
• NM_005336.6:c.-102-20824A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005336.6(HDLBP):​c.-102-20824A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,292 control chromosomes in the GnomAD database, including 1,187 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 0.11 (1187 hom., cov: 32)
• Consequence: HDLBP NM_005336.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005336.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HDLBP	NM_005336.6	MANE Select	c.-102-20824A>G		intron	N/A	NP_005327.1	A0A024R4E5
	HDLBP	NM_001320965.3		c.-102-20824A>G		intron	N/A	NP_001307894.1	Q00341-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HDLBP	ENST00000310931.10	TSL:1 MANE Select	c.-102-20824A>G		intron	N/A	ENSP00000312042.4	Q00341-1
	HDLBP	ENST00000875612.1		c.-102-20824A>G		intron	N/A	ENSP00000545671.1
	HDLBP	ENST00000944585.1		c.-102-20824A>G		intron	N/A	ENSP00000614644.1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16862 AN: 152174 Hom.: 1188 Cov.: 32

Gnomad AFR AF: 0.0323

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.111 AC: 16855 AN: 152292 Hom.: 1187 Cov.: 32 AF XY: 0.108 AC XY: 8064 AN XY: 74464

African (AFR) AF: 0.0322 AC: 1339 AN: 41574

American (AMR) AF: 0.145 AC: 2214 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3472

East Asian (EAS) AF: 0.115 AC: 596 AN: 5182

South Asian (SAS) AF: 0.0995 AC: 480 AN: 4824

European-Finnish (FIN) AF: 0.119 AC: 1260 AN: 10616

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10194 AN: 68014

Other (OTH) AF: 0.130 AC: 274 AN: 2114

Alfa AF: 0.140 Hom.: 641

Bravo AF: 0.106

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.62
PhyloP100		-0.10
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6752050; hg19: chr2-242228780;