rs872256

Variant names:

• chr9-2496480-T-A
• rs872256
• ENST00000416826.6:n.986-2178A>T

Variant summary

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

The ENST00000416826.6(VLDLR-AS1):​n.986-2178A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,914 control chromosomes in the GnomAD database, including 30,653 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 0.61 (30653 hom., cov: 31)
• Consequence: VLDLR-AS1 ENST00000416826.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 6 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.735 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.986-2178A>T		intron	N/A
	VLDLR-AS1	ENST00000447278.2	TSL:3	n.818-2178A>T		intron	N/A
	VLDLR-AS1	ENST00000648733.1		n.1093-2178A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93155 AN: 151796 Hom.: 30672 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.613 AC: 93147 AN: 151914 Hom.: 30653 Cov.: 31 AF XY: 0.616 AC XY: 45708 AN XY: 74234

African (AFR) AF: 0.362 AC: 14975 AN: 41396

American (AMR) AF: 0.607 AC: 9276 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2286 AN: 3470

East Asian (EAS) AF: 0.565 AC: 2917 AN: 5160

South Asian (SAS) AF: 0.756 AC: 3633 AN: 4808

European-Finnish (FIN) AF: 0.752 AC: 7925 AN: 10536

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49882 AN: 67958

Other (OTH) AF: 0.652 AC: 1376 AN: 2110

Alfa AF: 0.665 Hom.: 4327

Bravo AF: 0.592

Asia WGS AF: 0.588 AC: 2046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.041
DANN	Benign	0.49
PhyloP100		-1.7

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: rs872256;

hg19: chr9-2496480;