chr5-68789680-G-A

Variant names:

• chr5-68789680-G-A
• rs28155
• ENST00000843732.1:n.295-6184C>T

Variant summary

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

The ENST00000843732.1(LINC02198):​n.295-6184C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,940 control chromosomes in the GnomAD database, including 19,667 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 0.50 (19667 hom., cov: 31)
• Consequence: LINC02198 ENST00000843732.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• Publications: 2 publications found

Genes affected

LINC02198 (HGNC:53064): (long intergenic non-protein coding RNA 2198)

LOC105379013 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843732.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02198	ENST00000843732.1		n.295-6184C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75539 AN: 151822 Hom.: 19667 Cov.: 31

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.497 AC: 75559 AN: 151940 Hom.: 19667 Cov.: 31 AF XY: 0.502 AC XY: 37249 AN XY: 74248

African (AFR) AF: 0.330 AC: 13682 AN: 41430

American (AMR) AF: 0.487 AC: 7433 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2090 AN: 3472

East Asian (EAS) AF: 0.541 AC: 2793 AN: 5162

South Asian (SAS) AF: 0.605 AC: 2914 AN: 4816

European-Finnish (FIN) AF: 0.593 AC: 6240 AN: 10526

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38777 AN: 67968

Other (OTH) AF: 0.504 AC: 1061 AN: 2106

Alfa AF: 0.513 Hom.: 3291

Bravo AF: 0.480

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.71
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs28155; hg19: chr5-68085507;