rs1571812

Positions:

• chr9-2495870-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657742.1(VLDLR-AS1):​n.1029-1568G>T variant causes a intron, non coding transcript 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 ENST00000657742.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

Genes affected

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

LOC101930053 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC101930053	XR_007061396.1	n.253-1568G>T		intron_variant, non_coding_transcript_variant
LOC101930053	XR_007061397.1	n.372+623G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VLDLR-AS1	ENST00000657742.1	n.1029-1568G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.276

Alfa AF: 0.280 Hom.: 10438

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1571812; hg19: chr9-2495870;