rs729367

Variant names:

• chr9-2600253-A-G
• rs729367
• ENST00000453601.5:n.274+21847T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-2600253-A-G
• chr9-2600253-A-T

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+21847T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,084 control chromosomes in the GnomAD database, including 32,205 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 0.64 (32205 hom., cov: 32)
• Consequence: VLDLR-AS1 ENST00000453601.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453601.5. 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
	VLDLR-AS1	NR_015375.2		n.274+21847T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VLDLR-AS1	ENST00000453601.5	TSL:1	n.274+21847T>C		intron	N/A
	VLDLR-AS1	ENST00000416826.6	TSL:2	n.185+20976T>C		intron	N/A
	VLDLR-AS1	ENST00000447278.2	TSL:3	n.158+20976T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97714 AN: 151966 Hom.: 32174 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.643 AC: 97796 AN: 152084 Hom.: 32205 Cov.: 32 AF XY: 0.638 AC XY: 47440 AN XY: 74338

African (AFR) AF: 0.500 AC: 20770 AN: 41506

American (AMR) AF: 0.646 AC: 9867 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2620 AN: 3470

East Asian (EAS) AF: 0.522 AC: 2703 AN: 5180

South Asian (SAS) AF: 0.615 AC: 2959 AN: 4808

European-Finnish (FIN) AF: 0.693 AC: 7321 AN: 10564

Middle Eastern (MID) AF: 0.774 AC: 226 AN: 292

European-Non Finnish (NFE) AF: 0.724 AC: 49199 AN: 67968

Other (OTH) AF: 0.684 AC: 1444 AN: 2112

Alfa AF: 0.698 Hom.: 103536

Bravo AF: 0.634

Asia WGS AF: 0.515 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.57
PhyloP100		-0.91

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: rs729367;

hg19: chr9-2600253;