8-89795929-A-C

Variant names:

• chr8-89795929-A-C
• rs411279
• ENST00000814457.1:n.650-70288T>G

Variant summary

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

The ENST00000814457.1(PARAIL):​n.650-70288T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 151,910 control chromosomes in the GnomAD database, including 32,839 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 (32839 hom., cov: 31)
• Consequence: PARAIL ENST00000814457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 7 publications found

Genes affected

PARAIL (HGNC:55545): (palmitic acid regulated anti-inflammatory lncRNA)

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 = 0.877 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814457.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARAIL	ENST00000814457.1		n.650-70288T>G		intron	N/A
	PARAIL	ENST00000814510.1		n.246-31892T>G		intron	N/A
	PARAIL	ENST00000814511.1		n.518-31892T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96778 AN: 151790 Hom.: 32785 Cov.: 31

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.638 AC: 96890 AN: 151910 Hom.: 32839 Cov.: 31 AF XY: 0.634 AC XY: 47071 AN XY: 74242

African (AFR) AF: 0.884 AC: 36628 AN: 41430

American (AMR) AF: 0.522 AC: 7967 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1470 AN: 3466

East Asian (EAS) AF: 0.530 AC: 2737 AN: 5168

South Asian (SAS) AF: 0.437 AC: 2106 AN: 4818

European-Finnish (FIN) AF: 0.621 AC: 6528 AN: 10510

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.553 AC: 37580 AN: 67946

Other (OTH) AF: 0.613 AC: 1291 AN: 2106

Alfa AF: 0.562 Hom.: 12564

Bravo AF: 0.644

Asia WGS AF: 0.517 AC: 1794 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.9
DANN	Benign	0.87
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs411279; hg19: chr8-90808157;