rs919222

Variant names:

• chr5-153891596-G-A
• rs919222
• ENST00000509568.1:n.501+3945C>T

Variant summary

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

The ENST00000509568.1(LINC01861):​n.501+3945C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,080 control chromosomes in the GnomAD database, including 3,426 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 0.19 (3426 hom., cov: 32)
• Consequence: LINC01861 ENST00000509568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.497
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 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+3945C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01861	ENST00000509568.1	TSL:4	n.501+3945C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29382 AN: 151962 Hom.: 3416 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.0142

Gnomad SAS AF: 0.0474

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.193 AC: 29418 AN: 152080 Hom.: 3426 Cov.: 32 AF XY: 0.190 AC XY: 14134 AN XY: 74350

African (AFR) AF: 0.316 AC: 13079 AN: 41446

American (AMR) AF: 0.152 AC: 2327 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 650 AN: 3472

East Asian (EAS) AF: 0.0143 AC: 74 AN: 5186

South Asian (SAS) AF: 0.0464 AC: 224 AN: 4826

European-Finnish (FIN) AF: 0.200 AC: 2112 AN: 10570

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.151 AC: 10246 AN: 67974

Other (OTH) AF: 0.198 AC: 418 AN: 2112

Alfa AF: 0.208 Hom.: 1591

Bravo AF: 0.200

Asia WGS AF: 0.0690 AC: 240 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.28
PhyloP100		0.50

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: rs919222;

hg19: chr5-153271156;