rs1673101

Variant names:

• chr5-87738535-G-A
• rs1673101
• ENST00000815382.1:n.127-5559G>A

Variant summary

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

The ENST00000815382.1(LINC02488):​n.127-5559G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,822 control chromosomes in the GnomAD database, including 7,662 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 0.31 (7662 hom., cov: 32)
• Consequence: LINC02488 ENST00000815382.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 3 publications found

Genes affected

LINC02488 (HGNC:53467): (long intergenic non-protein coding RNA 2488)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815382.1. 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
	LINC02488	ENST00000815382.1		n.127-5559G>A		intron	N/A
	LINC02488	ENST00000815383.1		n.127-5559G>A		intron	N/A
	LINC02488	ENST00000815384.1		n.97-5559G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47694 AN: 151702 Hom.: 7633 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.315 AC: 47772 AN: 151822 Hom.: 7662 Cov.: 32 AF XY: 0.318 AC XY: 23558 AN XY: 74158

African (AFR) AF: 0.328 AC: 13555 AN: 41384

American (AMR) AF: 0.319 AC: 4864 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1112 AN: 3464

East Asian (EAS) AF: 0.247 AC: 1275 AN: 5158

South Asian (SAS) AF: 0.202 AC: 969 AN: 4808

European-Finnish (FIN) AF: 0.400 AC: 4218 AN: 10536

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.305 AC: 20704 AN: 67896

Other (OTH) AF: 0.328 AC: 692 AN: 2108

Alfa AF: 0.310 Hom.: 4255

Bravo AF: 0.312

Asia WGS AF: 0.269 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	2.3
DANN	Benign	0.81
PhyloP100		-0.44

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: rs1673101;

hg19: chr5-87034352;