rs729367

chr9-2600253-A-Gchr9-2600253-A-T

Variant summary

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

The NR_015375.2(VLDLR-AS1):n.274+21847T>C 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 0.643 in 152,084 control chromosomes in the GnomAD database, including 32,205 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 0.64 (32205 hom., cov: 32)
• Consequence: VLDLR-AS1 NR_015375.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VLDLR-AS1	NR_015375.2	n.274+21847T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VLDLR-AS1	ENST00000657742.1	n.274+21847T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97714 AN: 151966 Hom.: 32174 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.643 AC: 97796 AN: 152084 Hom.: 32205 Cov.: 32 AF XY: 0.638 AC XY: 47440 AN XY: 74338

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.684

Alfa AF: 0.716 Hom.: 64463

Bravo AF: 0.634

Asia WGS AF: 0.515 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.18
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs729367; hg19: chr9-2600253;