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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101930053	XR_007061396.1	n.253-1568G>T		intron_variant	Intron 2 of 3
LOC101930053	XR_007061397.1	n.372+623G>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VLDLR-AS1	ENST00000416826.6	n.986-1568G>T		intron_variant	Intron 7 of 10	2
VLDLR-AS1	ENST00000447278.2	n.818-1568G>T		intron_variant	Intron 6 of 9	3
VLDLR-AS1	ENST00000648733.1	n.1093-1568G>T		intron_variant	Intron 8 of 11

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 v4.3

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;