9-2496480-T-A

Position:

• chr9-2496480-T-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

VLDLR-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101930053	XR_007061396.1	n.253-2178A>T		intron_variant
LOC101930053	XR_007061397.1	n.372+13A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VLDLR-AS1	ENST00000416826.6	n.986-2178A>T		intron_variant		2
VLDLR-AS1	ENST00000447278.2	n.818-2178A>T		intron_variant		3
VLDLR-AS1	ENST00000648733.1	n.1093-2178A>T		intron_variant

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

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.734

Gnomad4 OTH AF: 0.652

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs872256; hg19: chr9-2496480;