rs9304608

Variant names:

• chr19-42693429-C-T
• rs9304608
• ENST00000750098.1:n.240-5255C>T

Variant summary

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

The ENST00000750098.1(LIPE-AS1):​n.240-5255C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,132 control chromosomes in the GnomAD database, including 5,507 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 0.21 (5507 hom., cov: 32)
• Consequence: LIPE-AS1 ENST00000750098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 6 publications found

Genes affected

LIPE-AS1 (HGNC:48589): (LIPE antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPE-AS1	ENST00000750098.1	n.240-5255C>T		intron_variant	Intron 3 of 4
LIPE-AS1	ENST00000750099.1	n.287-5255C>T		intron_variant	Intron 3 of 3
LIPE-AS1	ENST00000750203.1	n.216+39166C>T		intron_variant	Intron 1 of 3
LIPE-AS1	ENST00000750204.1	n.165+39166C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31138 AN: 152014 Hom.: 5472 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0902

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0845

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0869

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.205 AC: 31232 AN: 152132 Hom.: 5507 Cov.: 32 AF XY: 0.202 AC XY: 15009 AN XY: 74360

African (AFR) AF: 0.482 AC: 19961 AN: 41436

American (AMR) AF: 0.168 AC: 2567 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3470

East Asian (EAS) AF: 0.0902 AC: 467 AN: 5178

South Asian (SAS) AF: 0.113 AC: 544 AN: 4828

European-Finnish (FIN) AF: 0.0845 AC: 896 AN: 10604

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0869 AC: 5906 AN: 68000

Other (OTH) AF: 0.185 AC: 391 AN: 2110

Alfa AF: 0.122 Hom.: 2042

Bravo AF: 0.224

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.25
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs9304608; hg19: chr19-43197581;