ENST00000814513.1:n.1010G>C

Variant names:

• chr8-89626244-C-G
• rs4961149
• ENST00000814513.1:n.1010G>C

Variant summary

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

The ENST00000814513.1(PARAIL):​n.1010G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,998 control chromosomes in the GnomAD database, including 10,905 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 0.34 (10905 hom., cov: 32)
• Consequence: PARAIL ENST00000814513.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.770
• Publications: 1 publications found

Genes affected

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

LOC112268015 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814513.1. 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	ENST00000814513.1		n.1010G>C		non_coding_transcript_exon	Exon 4 of 4
	PARAIL	ENST00000519655.6	TSL:5	n.946+1911G>C		intron	N/A
	PARAIL	ENST00000524190.3	TSL:3	n.875+1911G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51817 AN: 151880 Hom.: 10896 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.341 AC: 51844 AN: 151998 Hom.: 10905 Cov.: 32 AF XY: 0.352 AC XY: 26160 AN XY: 74286

African (AFR) AF: 0.101 AC: 4186 AN: 41486

American (AMR) AF: 0.453 AC: 6914 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1751 AN: 3468

East Asian (EAS) AF: 0.701 AC: 3623 AN: 5172

South Asian (SAS) AF: 0.559 AC: 2692 AN: 4820

European-Finnish (FIN) AF: 0.405 AC: 4275 AN: 10556

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27058 AN: 67938

Other (OTH) AF: 0.360 AC: 754 AN: 2096

Alfa AF: 0.243 Hom.: 641

Bravo AF: 0.330

Asia WGS AF: 0.556 AC: 1933 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.57
PhyloP100		0.77

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4961149;

hg19: chr8-90638473;