chr5-69030471-T-C

Variant names:

• chr5-69030471-T-C
• rs3923114
• ENST00000696797.1:n.466+8048A>G

Variant summary

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

The ENST00000696797.1(LINC02198):​n.466+8048A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,110 control chromosomes in the GnomAD database, including 8,645 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 0.30 (8645 hom., cov: 32)
• Consequence: LINC02198 ENST00000696797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.425 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	ENST00000696797.1	n.466+8048A>G		intron_variant	Intron 2 of 4
LINC02198	ENST00000717716.1	n.485-308A>G		intron_variant	Intron 1 of 3
LINC02198	ENST00000717717.1	n.614-308A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45378 AN: 151992 Hom.: 8647 Cov.: 32

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.298 AC: 45374 AN: 152110 Hom.: 8645 Cov.: 32 AF XY: 0.294 AC XY: 21844 AN XY: 74362

African (AFR) AF: 0.0792 AC: 3287 AN: 41524

American (AMR) AF: 0.434 AC: 6623 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1712 AN: 3470

East Asian (EAS) AF: 0.131 AC: 680 AN: 5174

South Asian (SAS) AF: 0.192 AC: 926 AN: 4828

European-Finnish (FIN) AF: 0.330 AC: 3492 AN: 10568

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27682 AN: 67954

Other (OTH) AF: 0.327 AC: 691 AN: 2114

Alfa AF: 0.329 Hom.: 1238

Bravo AF: 0.301

Asia WGS AF: 0.182 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.74
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs3923114; hg19: chr5-68326298;