rs1571812

Variant names:

• chr9-2495870-C-A
• rs1571812
• ENST00000416826.6:n.986-1568G>T

Variant summary

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

The ENST00000416826.6(VLDLR-AS1):​n.986-1568G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,058 control chromosomes in the GnomAD database, including 5,178 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 0.25 (5178 hom., cov: 32)
• Consequence: VLDLR-AS1 ENST00000416826.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840
• Publications: 4 publications found

Genes affected

VLDLR-AS1 (HGNC:49621): (VLDLR antisense RNA 1)

LOC101930053 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416826.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VLDLR-AS1	ENST00000416826.6	TSL:2	n.986-1568G>T		intron	N/A
	VLDLR-AS1	ENST00000447278.2	TSL:3	n.818-1568G>T		intron	N/A
	VLDLR-AS1	ENST00000648733.1		n.1093-1568G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38388 AN: 151940 Hom.: 5180 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.252 AC: 38383 AN: 152058 Hom.: 5178 Cov.: 32 AF XY: 0.255 AC XY: 18951 AN XY: 74318

African (AFR) AF: 0.161 AC: 6697 AN: 41496

American (AMR) AF: 0.249 AC: 3798 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 997 AN: 3464

East Asian (EAS) AF: 0.456 AC: 2344 AN: 5144

South Asian (SAS) AF: 0.385 AC: 1855 AN: 4812

European-Finnish (FIN) AF: 0.266 AC: 2808 AN: 10572

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19013 AN: 67978

Other (OTH) AF: 0.276 AC: 582 AN: 2108

Alfa AF: 0.273 Hom.: 23487

Bravo AF: 0.245

Asia WGS AF: 0.373 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.72
PhyloP100		-0.84

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1571812; hg19: chr9-2495870;