rs39765

Variant names:

• chr8-89791496-G-A
• rs39765
• ENST00000814457.1:n.650-65855C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-89791496-G-A
• chr8-89791496-G-C

Variant summary

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

The ENST00000814457.1(PARAIL):​n.650-65855C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,970 control chromosomes in the GnomAD database, including 6,124 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 (6124 hom., cov: 32)
• Consequence: PARAIL ENST00000814457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARAIL	ENST00000814457.1	n.650-65855C>T		intron_variant	Intron 2 of 3
PARAIL	ENST00000814510.1	n.246-27459C>T		intron_variant	Intron 2 of 2
PARAIL	ENST00000814511.1	n.518-27459C>T		intron_variant	Intron 2 of 2
PARAIL	ENST00000814512.1	n.258-27459C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38565 AN: 151852 Hom.: 6124 Cov.: 32

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.254 AC: 38566 AN: 151970 Hom.: 6124 Cov.: 32 AF XY: 0.251 AC XY: 18679 AN XY: 74274

African (AFR) AF: 0.0792 AC: 3286 AN: 41484

American (AMR) AF: 0.275 AC: 4202 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 930 AN: 3468

East Asian (EAS) AF: 0.0411 AC: 213 AN: 5186

South Asian (SAS) AF: 0.203 AC: 977 AN: 4824

European-Finnish (FIN) AF: 0.371 AC: 3905 AN: 10538

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24235 AN: 67900

Other (OTH) AF: 0.246 AC: 517 AN: 2102

Alfa AF: 0.319 Hom.: 35110

Bravo AF: 0.239

Asia WGS AF: 0.127 AC: 441 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.45
DANN	Benign	0.47
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs39765; hg19: chr8-90803724;