rs28155

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-68789680-G-A
• chr5-68789680-G-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379013	XR_007058804.1	n.440+39028C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02198	ENST00000843732.1	n.295-6184C>T		intron_variant	Intron 2 of 2

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 v4.3

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;