chr9-2425857-C-G

Variant names:

• chr9-2425857-C-G
• rs10491710
• ENST00000653709.1:n.101G>C

Variant summary

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

The ENST00000653709.1(VLDLR-AS1):​n.101G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,048 control chromosomes in the GnomAD database, including 28,284 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 0.60 (28284 hom., cov: 32)
• Consequence: VLDLR-AS1 ENST00000653709.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417
• Publications: 2 publications found

Genes affected

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

ENSG00000296869 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101930053	XR_001746602.3	n.194-317G>C		intron_variant	Intron 3 of 4
LOC101930053	XR_001746603.2	n.437-317G>C		intron_variant	Intron 3 of 5
LOC101930053	XR_001746604.2	n.885-317G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VLDLR-AS1	ENST00000653709.1	n.101G>C		non_coding_transcript_exon_variant	Exon 1 of 2
VLDLR-AS1	ENST00000416826.6	n.1215-317G>C		intron_variant	Intron 9 of 10	2
VLDLR-AS1	ENST00000447278.2	n.1127-321G>C		intron_variant	Intron 8 of 9	3

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91163 AN: 151930 Hom.: 28270 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.600 AC: 91217 AN: 152048 Hom.: 28284 Cov.: 32 AF XY: 0.599 AC XY: 44501 AN XY: 74334

African (AFR) AF: 0.447 AC: 18516 AN: 41458

American (AMR) AF: 0.665 AC: 10152 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2280 AN: 3472

East Asian (EAS) AF: 0.845 AC: 4368 AN: 5168

South Asian (SAS) AF: 0.676 AC: 3252 AN: 4808

European-Finnish (FIN) AF: 0.594 AC: 6281 AN: 10576

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44275 AN: 67992

Other (OTH) AF: 0.586 AC: 1238 AN: 2112

Alfa AF: 0.517 Hom.: 1522

Bravo AF: 0.600

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.3
DANN	Benign	0.79
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10491710; hg19: chr9-2425857;