chr8-89745593-T-G

Variant names:

• chr8-89745593-T-G
• rs13276910
• ENST00000504145.7:n.667+11452A>C

Variant summary

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

The ENST00000504145.7(PARAIL):​n.667+11452A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,182 control chromosomes in the GnomAD database, including 5,840 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 0.25 (5840 hom., cov: 32)
• Consequence: PARAIL ENST00000504145.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 3 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504145.7. 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
	PARAIL	NR_125822.1		n.667+11452A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARAIL	ENST00000504145.7	TSL:3	n.667+11452A>C		intron	N/A
	PARAIL	ENST00000519655.6	TSL:5	n.683+11452A>C		intron	N/A
	PARAIL	ENST00000521996.3	TSL:3	n.528+11452A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37923 AN: 152064 Hom.: 5838 Cov.: 32

Gnomad AFR AF: 0.0873

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.0413

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.249 AC: 37929 AN: 152182 Hom.: 5840 Cov.: 32 AF XY: 0.246 AC XY: 18283 AN XY: 74404

African (AFR) AF: 0.0871 AC: 3618 AN: 41544

American (AMR) AF: 0.262 AC: 4011 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 858 AN: 3468

East Asian (EAS) AF: 0.0414 AC: 215 AN: 5188

South Asian (SAS) AF: 0.201 AC: 968 AN: 4822

European-Finnish (FIN) AF: 0.351 AC: 3711 AN: 10576

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23739 AN: 67978

Other (OTH) AF: 0.244 AC: 514 AN: 2110

Alfa AF: 0.302 Hom.: 1692

Bravo AF: 0.236

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.38
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs13276910; hg19: chr8-90757821;