9-2572909-C-T

Variant names:

• chr9-2572909-C-T
• rs502309
• ENST00000453601.5:n.275-33357G>A

Variant summary

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

The ENST00000453601.5(VLDLR-AS1):​n.275-33357G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 152,228 control chromosomes in the GnomAD database, including 64,934 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 0.92 (64934 hom., cov: 33)
• Consequence: VLDLR-AS1 ENST00000453601.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VLDLR-AS1	NR_015375.2	n.275-33357G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VLDLR-AS1	ENST00000453601.5	n.275-33357G>A		intron_variant	Intron 1 of 3	1
VLDLR-AS1	ENST00000416826.6	n.186-33357G>A		intron_variant	Intron 1 of 10	2
VLDLR-AS1	ENST00000447278.2	n.159-33357G>A		intron_variant	Intron 1 of 9	3

Frequencies

GnomAD3 genomes AF: 0.919 AC: 139774 AN: 152110 Hom.: 64887 Cov.: 33

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.992

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.978

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.919 AC: 139880 AN: 152228 Hom.: 64934 Cov.: 33 AF XY: 0.921 AC XY: 68584 AN XY: 74444

African (AFR) AF: 0.765 AC: 31734 AN: 41478

American (AMR) AF: 0.962 AC: 14722 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3430 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5183 AN: 5186

South Asian (SAS) AF: 0.993 AC: 4790 AN: 4826

European-Finnish (FIN) AF: 0.973 AC: 10333 AN: 10616

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.978 AC: 66521 AN: 68036

Other (OTH) AF: 0.938 AC: 1982 AN: 2112

Alfa AF: 0.944 Hom.: 8481

Bravo AF: 0.910

Asia WGS AF: 0.978 AC: 3399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.4
DANN	Benign	0.72
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs502309; hg19: chr9-2572909;