rs10113968

Variant names:

• chr9-2455202-T-G
• rs10113968
• ENST00000416826.6:n.1215-29662A>C

Variant summary

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

The ENST00000416826.6(VLDLR-AS1):​n.1215-29662A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,856 control chromosomes in the GnomAD database, including 17,529 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 0.47 (17529 hom., cov: 32)
• Consequence: VLDLR-AS1 ENST00000416826.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 0 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 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.1215-29662A>C		intron	N/A
	VLDLR-AS1	ENST00000447278.2	TSL:3	n.1127-29666A>C		intron	N/A
	VLDLR-AS1	ENST00000648733.1		n.1402-29662A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71663 AN: 151736 Hom.: 17507 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.472 AC: 71733 AN: 151856 Hom.: 17529 Cov.: 32 AF XY: 0.470 AC XY: 34859 AN XY: 74218

African (AFR) AF: 0.395 AC: 16339 AN: 41394

American (AMR) AF: 0.411 AC: 6261 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1580 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1035 AN: 5146

South Asian (SAS) AF: 0.426 AC: 2051 AN: 4818

European-Finnish (FIN) AF: 0.552 AC: 5832 AN: 10568

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 36975 AN: 67902

Other (OTH) AF: 0.460 AC: 973 AN: 2114

Alfa AF: 0.504 Hom.: 12500

Bravo AF: 0.459

Asia WGS AF: 0.290 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.2
DANN	Benign	0.84
PhyloP100		0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10113968;

hg19: chr9-2455202;