19-42641265-A-G

Variant names:

• chr19-42641265-A-G
• rs10407775
• ENST00000594624.8:n.234-9822A>G

Variant summary

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

The ENST00000594624.8(LIPE-AS1):​n.234-9822A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,212 control chromosomes in the GnomAD database, including 3,334 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 0.18 (3334 hom., cov: 32)
• Consequence: LIPE-AS1 ENST00000594624.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000594624.8. 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
	LIPE-AS1	NR_073179.1		n.1451-9822A>G		intron	N/A
	LIPE-AS1	NR_073180.1		n.206-9822A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPE-AS1	ENST00000594624.8	TSL:1	n.234-9822A>G		intron	N/A
	LIPE-AS1	ENST00000594688.1	TSL:2	n.1451-9822A>G		intron	N/A
	LIPE-AS1	ENST00000661814.1		n.261-9822A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27092 AN: 152094 Hom.: 3315 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.178 AC: 27152 AN: 152212 Hom.: 3334 Cov.: 32 AF XY: 0.179 AC XY: 13346 AN XY: 74424

African (AFR) AF: 0.340 AC: 14097 AN: 41502

American (AMR) AF: 0.232 AC: 3545 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 564 AN: 3470

East Asian (EAS) AF: 0.106 AC: 552 AN: 5190

South Asian (SAS) AF: 0.211 AC: 1021 AN: 4828

European-Finnish (FIN) AF: 0.0781 AC: 828 AN: 10604

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.0898 AC: 6108 AN: 68004

Other (OTH) AF: 0.166 AC: 350 AN: 2114

Alfa AF: 0.101 Hom.: 253

Bravo AF: 0.195

Asia WGS AF: 0.159 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.24
DANN	Benign	0.59
PhyloP100		-3.0

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: rs10407775;

hg19: chr19-43145417;