9-2506236-G-T

Variant names:

• chr9-2506236-G-T
• rs10491713
• ENST00000416826.6:n.985+183C>A

Variant summary

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

The ENST00000416826.6(VLDLR-AS1):​n.985+183C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,048 control chromosomes in the GnomAD database, including 2,863 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 0.19 (2863 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: VLDLR-AS1 ENST00000416826.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VLDLR-AS1	ENST00000416826.6	TSL:2	n.985+183C>A		intron	N/A
	VLDLR-AS1	ENST00000447278.2	TSL:3	n.683+183C>A		intron	N/A
	VLDLR-AS1	ENST00000648733.1		n.958+183C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28276 AN: 151928 Hom.: 2862 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.197

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.186 AC: 28274 AN: 152046 Hom.: 2863 Cov.: 32 AF XY: 0.185 AC XY: 13782 AN XY: 74328

African (AFR) AF: 0.135 AC: 5605 AN: 41458

American (AMR) AF: 0.187 AC: 2858 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3466

East Asian (EAS) AF: 0.382 AC: 1976 AN: 5176

South Asian (SAS) AF: 0.189 AC: 912 AN: 4820

European-Finnish (FIN) AF: 0.174 AC: 1837 AN: 10558

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.202 AC: 13730 AN: 67974

Other (OTH) AF: 0.201 AC: 424 AN: 2114

Alfa AF: 0.178 Hom.: 1460

Bravo AF: 0.186

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10491713; hg19: chr9-2506236;