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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101930053	XR_001746602.3	n.151-2211A>C		intron_variant	Intron 2 of 4
LOC101930053	XR_001746603.2	n.394-2211A>C		intron_variant	Intron 2 of 5
LOC101930053	XR_428440.3	n.394-29662A>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VLDLR-AS1	ENST00000416826.6	n.1215-29662A>C		intron_variant	Intron 9 of 10	2
VLDLR-AS1	ENST00000447278.2	n.1127-29666A>C		intron_variant	Intron 8 of 9	3
VLDLR-AS1	ENST00000648733.1	n.1402-29662A>C		intron_variant	Intron 10 of 11

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 v4.3

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

Other links and lift over

dbSNP: rs10113968; hg19: chr9-2455202;