chr9-2551654-T-C

Variant names:

• chr9-2551654-T-C
• rs12237653
• ENST00000453601.5:n.275-12102A>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.275-12102A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,132 control chromosomes in the GnomAD database, including 2,641 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 0.17 (2641 hom., cov: 32)
• Consequence: VLDLR-AS1 ENST00000453601.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VLDLR-AS1	NR_015375.2	n.275-12102A>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.275-12102A>G		intron_variant	Intron 1 of 3	1
VLDLR-AS1	ENST00000416826.6	n.186-12102A>G		intron_variant	Intron 1 of 10	2
VLDLR-AS1	ENST00000424605.5	n.134-12102A>G		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26190 AN: 152014 Hom.: 2630 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.0868

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.173 AC: 26243 AN: 152132 Hom.: 2641 Cov.: 32 AF XY: 0.178 AC XY: 13246 AN XY: 74370

African (AFR) AF: 0.192 AC: 7957 AN: 41476

American (AMR) AF: 0.252 AC: 3846 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0868 AC: 301 AN: 3468

East Asian (EAS) AF: 0.439 AC: 2270 AN: 5174

South Asian (SAS) AF: 0.166 AC: 802 AN: 4820

European-Finnish (FIN) AF: 0.128 AC: 1360 AN: 10602

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9230 AN: 67994

Other (OTH) AF: 0.169 AC: 357 AN: 2110

Alfa AF: 0.154 Hom.: 3368

Bravo AF: 0.185

Asia WGS AF: 0.354 AC: 1228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.87
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs12237653; hg19: chr9-2551654;