rs10185319

Variant names:

• chr2-241314580-C-A
• rs10185319
• NM_005336.6:c.-103+990G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_005336.6(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 NM_005336.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 12 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=-0.8).
• 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 rank	MANE	Protein	UniProt
HDLBP	NM_005336.6	c.-103+990G>T		intron_variant	Intron 1 of 27	ENST00000310931.10	NP_005327.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HDLBP	ENST00000310931.10	c.-103+990G>T		intron_variant	Intron 1 of 27	1	NM_005336.6	ENSP00000312042.4

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

African (AFR) AF: 0.782 AC: 32404 AN: 41442

American (AMR) AF: 0.858 AC: 13122 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2975 AN: 3470

East Asian (EAS) AF: 0.947 AC: 4907 AN: 5182

South Asian (SAS) AF: 0.702 AC: 3379 AN: 4816

European-Finnish (FIN) AF: 0.816 AC: 8617 AN: 10560

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53545 AN: 67964

Other (OTH) AF: 0.825 AC: 1745 AN: 2114

Alfa AF: 0.799 Hom.: 169147

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
PhyloP100		0.0050
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: rs10185319; hg19: chr2-242253995;