rs919221

Variant names:

• chr5-153891516-C-T
• rs919221
• ENST00000509568.1:n.501+4025G>A

Variant summary

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

The ENST00000509568.1(LINC01861):​n.501+4025G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,000 control chromosomes in the GnomAD database, including 23,408 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 0.55 (23408 hom., cov: 32)
• Consequence: LINC01861 ENST00000509568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 4 publications found

Genes affected

LINC01861 (HGNC:52680): (long intergenic non-protein coding RNA 1861)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509568.1. 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
	LINC01861	NR_146729.1		n.501+4025G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01861	ENST00000509568.1	TSL:4	n.501+4025G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83739 AN: 151880 Hom.: 23368 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.552 AC: 83829 AN: 152000 Hom.: 23408 Cov.: 32 AF XY: 0.556 AC XY: 41329 AN XY: 74304

African (AFR) AF: 0.622 AC: 25792 AN: 41466

American (AMR) AF: 0.581 AC: 8881 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1713 AN: 3470

East Asian (EAS) AF: 0.707 AC: 3655 AN: 5168

South Asian (SAS) AF: 0.518 AC: 2500 AN: 4822

European-Finnish (FIN) AF: 0.606 AC: 6395 AN: 10560

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33091 AN: 67928

Other (OTH) AF: 0.541 AC: 1139 AN: 2106

Alfa AF: 0.541 Hom.: 4324

Bravo AF: 0.558

Asia WGS AF: 0.599 AC: 2081 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.078
DANN	Benign	0.13
PhyloP100		-2.2

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: rs919221;

hg19: chr5-153271076;