chr8-89824005-C-T

Variant names:

• chr8-89824005-C-T
• rs39770
• ENST00000814457.1:n.649+75342G>A

Variant summary

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

The ENST00000814457.1(PARAIL):​n.649+75342G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 151,838 control chromosomes in the GnomAD database, including 7,320 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 0.30 (7320 hom., cov: 32)
• Consequence: PARAIL ENST00000814457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.917
• Publications: 4 publications found

Genes affected

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

COX6B1P6 (HGNC:37676): (cytochrome c oxidase subunit 6B1 pseudogene 6)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.363 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.649+75342G>A		intron	N/A
	PARAIL	ENST00000814510.1		n.246-59968G>A		intron	N/A
	PARAIL	ENST00000814511.1		n.518-59968G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44845 AN: 151720 Hom.: 7326 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.0407

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.295 AC: 44837 AN: 151838 Hom.: 7320 Cov.: 32 AF XY: 0.292 AC XY: 21679 AN XY: 74180

African (AFR) AF: 0.213 AC: 8812 AN: 41426

American (AMR) AF: 0.237 AC: 3626 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 901 AN: 3428

East Asian (EAS) AF: 0.0408 AC: 211 AN: 5174

South Asian (SAS) AF: 0.251 AC: 1207 AN: 4808

European-Finnish (FIN) AF: 0.410 AC: 4307 AN: 10506

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.366 AC: 24884 AN: 67920

Other (OTH) AF: 0.267 AC: 562 AN: 2104

Alfa AF: 0.341 Hom.: 5433

Bravo AF: 0.277

Asia WGS AF: 0.143 AC: 497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.88
DANN	Benign	0.36
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs39770; hg19: chr8-90836233;