5-68896913-C-T

Variant names:

• chr5-68896913-C-T
• rs4976053
• ENST00000503268.2:n.541+63627G>A

Variant summary

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

The ENST00000503268.2(LINC02198):​n.541+63627G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,104 control chromosomes in the GnomAD database, including 37,623 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 0.70 (37623 hom., cov: 33)
• Consequence: LINC02198 ENST00000503268.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02198	ENST00000503268.2	n.541+63627G>A		intron_variant	Intron 3 of 3	3
LINC02198	ENST00000668535.3	n.578+63627G>A		intron_variant	Intron 3 of 5
LINC02198	ENST00000690326.3	n.255-68084G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106610 AN: 151986 Hom.: 37595 Cov.: 33

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.701 AC: 106698 AN: 152104 Hom.: 37623 Cov.: 33 AF XY: 0.704 AC XY: 52343 AN XY: 74356

African (AFR) AF: 0.749 AC: 31080 AN: 41490

American (AMR) AF: 0.753 AC: 11512 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2530 AN: 3470

East Asian (EAS) AF: 0.666 AC: 3440 AN: 5168

South Asian (SAS) AF: 0.622 AC: 2996 AN: 4814

European-Finnish (FIN) AF: 0.705 AC: 7465 AN: 10582

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45589 AN: 67982

Other (OTH) AF: 0.688 AC: 1450 AN: 2108

Alfa AF: 0.695 Hom.: 11733

Bravo AF: 0.708

Asia WGS AF: 0.628 AC: 2185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.38
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs4976053; hg19: chr5-68192740;