9-2534779-A-G

Variant names:

• chr9-2534779-A-G
• rs1996055
• ENST00000416826.6:n.434+1580T>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.434+1580T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,296 control chromosomes in the GnomAD database, including 918 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 0.10 (918 hom., cov: 33)
• Consequence: VLDLR-AS1 ENST00000416826.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• 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=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.117 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.434+1580T>C		intron	N/A
	VLDLR-AS1	ENST00000447278.2	TSL:3	n.312+4620T>C		intron	N/A
	VLDLR-AS1	ENST00000648733.1		n.407+1580T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15972 AN: 152178 Hom.: 916 Cov.: 33

Gnomad AFR AF: 0.0916

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0822

Gnomad EAS AF: 0.0165

Gnomad SAS AF: 0.0641

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0924

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

GnomAD4 genome AF: 0.105 AC: 15991 AN: 152296 Hom.: 918 Cov.: 33 AF XY: 0.105 AC XY: 7808 AN XY: 74460

African (AFR) AF: 0.0916 AC: 3807 AN: 41562

American (AMR) AF: 0.122 AC: 1867 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0822 AC: 285 AN: 3468

East Asian (EAS) AF: 0.0166 AC: 86 AN: 5194

South Asian (SAS) AF: 0.0639 AC: 309 AN: 4834

European-Finnish (FIN) AF: 0.155 AC: 1639 AN: 10600

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7676 AN: 68024

Other (OTH) AF: 0.0915 AC: 193 AN: 2110

Alfa AF: 0.112 Hom.: 1871

Bravo AF: 0.105

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.6
DANN	Benign	0.86
PhyloP100		0.072

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: rs1996055;

hg19: chr9-2534779;

COSMIC: COSV69613587;