9-2618969-T-C

Variant names:

• chr9-2618969-T-C
• rs4741746
• ENST00000453601.5:n.274+3131A>G

Variant summary

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

The ENST00000453601.5(VLDLR-AS1):​n.274+3131A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,100 control chromosomes in the GnomAD database, including 2,133 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 0.16 (2133 hom., cov: 32)
• Consequence: VLDLR-AS1 ENST00000453601.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VLDLR-AS1	NR_015375.2	n.274+3131A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VLDLR-AS1	ENST00000453601.5	n.274+3131A>G		intron_variant	Intron 1 of 3	1
VLDLR-AS1	ENST00000416826.6	n.185+2260A>G		intron_variant	Intron 1 of 10	2
VLDLR-AS1	ENST00000447278.2	n.158+2260A>G		intron_variant	Intron 1 of 9	3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24108 AN: 151982 Hom.: 2123 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.159 AC: 24156 AN: 152100 Hom.: 2133 Cov.: 32 AF XY: 0.162 AC XY: 12078 AN XY: 74346

African (AFR) AF: 0.171 AC: 7102 AN: 41482

American (AMR) AF: 0.195 AC: 2982 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 613 AN: 3472

East Asian (EAS) AF: 0.368 AC: 1896 AN: 5150

South Asian (SAS) AF: 0.202 AC: 974 AN: 4810

European-Finnish (FIN) AF: 0.149 AC: 1573 AN: 10582

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8458 AN: 68004

Other (OTH) AF: 0.182 AC: 385 AN: 2112

Alfa AF: 0.140 Hom.: 6390

Bravo AF: 0.162

Asia WGS AF: 0.254 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.69
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs4741746; hg19: chr9-2618969;