chr2-241282982-A-G

Variant names:

• chr2-241282982-A-G
• rs6724257
• NM_005336.6:c.-102-14441T>C

Variant summary

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

The NM_005336.6(HDLBP):​c.-102-14441T>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
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 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.-102-14441T>C		intron	N/A	NP_005327.1	A0A024R4E5
	HDLBP	NM_001320965.3		c.-102-14441T>C		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.-102-14441T>C		intron	N/A	ENSP00000312042.4	Q00341-1
	HDLBP	ENST00000875612.1		c.-102-14441T>C		intron	N/A	ENSP00000545671.1
	HDLBP	ENST00000944585.1		c.-102-14441T>C		intron	N/A	ENSP00000614644.1

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

African (AFR) AF: 0.181 AC: 7526 AN: 41524

American (AMR) AF: 0.282 AC: 4314 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1349 AN: 3468

East Asian (EAS) AF: 0.513 AC: 2654 AN: 5170

South Asian (SAS) AF: 0.437 AC: 2108 AN: 4822

European-Finnish (FIN) AF: 0.391 AC: 4136 AN: 10566

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25905 AN: 67994

Other (OTH) AF: 0.322 AC: 679 AN: 2110

Alfa AF: 0.375 Hom.: 9017

Bravo AF: 0.304

Asia WGS AF: 0.462 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.71
PhyloP100		-0.50
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: rs6724257; hg19: chr2-242222397;