rs218949

Variant names:

• chr8-89708239-T-C
• rs218949
• ENST00000519655.6:n.683+48806A>G

Variant summary

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

The ENST00000524190.3(PARAIL):​n.632+48806A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,056 control chromosomes in the GnomAD database, including 7,002 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 0.28 (7002 hom., cov: 32)
• Consequence: PARAIL ENST00000524190.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524190.3. 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	ENST00000519655.6	TSL:5	n.683+48806A>G		intron	N/A
	PARAIL	ENST00000524190.3	TSL:3	n.632+48806A>G		intron	N/A
	PARAIL	ENST00000656898.3		n.811+16390A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42299 AN: 151938 Hom.: 6998 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0424

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.278 AC: 42314 AN: 152056 Hom.: 7002 Cov.: 32 AF XY: 0.271 AC XY: 20156 AN XY: 74304

African (AFR) AF: 0.127 AC: 5256 AN: 41486

American (AMR) AF: 0.294 AC: 4497 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 958 AN: 3472

East Asian (EAS) AF: 0.0425 AC: 220 AN: 5176

South Asian (SAS) AF: 0.180 AC: 868 AN: 4812

European-Finnish (FIN) AF: 0.344 AC: 3630 AN: 10558

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26040 AN: 67950

Other (OTH) AF: 0.269 AC: 566 AN: 2108

Alfa AF: 0.329 Hom.: 1201

Bravo AF: 0.267

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.17
PhyloP100		0.12

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: rs218949;

hg19: chr8-90720467;