rs10407775

chr19-42641265-A-Gchr19-42641265-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_073180.1(LIPE-AS1):n.206-9822A>G variant causes a intron, non coding transcript 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 NR_073180.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LIPE-AS1	NR_073180.1	n.206-9822A>G		intron_variant, non_coding_transcript_variant
LIPE-AS1	NR_073179.1	n.1451-9822A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIPE-AS1	ENST00000594624.7	n.195-9822A>G		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.0898

Gnomad4 OTH AF: 0.166

Alfa AF: 0.0918 Hom.: 205

Bravo AF: 0.195

Asia WGS AF: 0.159 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.24
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10407775; hg19: chr19-43145417;