chr5-8891398-T-C

Variant names:

• chr5-8891398-T-C
• rs11948993
• ENST00000651480.1:n.614-1656T>C

Variant summary

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

The ENST00000651480.1(LINC02199):​n.614-1656T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,010 control chromosomes in the GnomAD database, including 13,138 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 0.39 (13138 hom., cov: 31)
• Consequence: LINC02199 ENST00000651480.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 3 publications found

Genes affected

LINC02199 (HGNC:53065): (long intergenic non-protein coding RNA 2199)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 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
LINC02199	ENST00000651480.1	n.614-1656T>C		intron_variant	Intron 3 of 3
LINC02199	ENST00000796093.1	n.414-6367T>C		intron_variant	Intron 3 of 3
LINC02199	ENST00000796095.1	n.576-1656T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58578 AN: 151892 Hom.: 13094 Cov.: 31

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.386 AC: 58677 AN: 152010 Hom.: 13138 Cov.: 31 AF XY: 0.380 AC XY: 28250 AN XY: 74306

African (AFR) AF: 0.630 AC: 26117 AN: 41464

American (AMR) AF: 0.311 AC: 4749 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3472

East Asian (EAS) AF: 0.239 AC: 1232 AN: 5162

South Asian (SAS) AF: 0.411 AC: 1972 AN: 4800

European-Finnish (FIN) AF: 0.221 AC: 2342 AN: 10574

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20116 AN: 67942

Other (OTH) AF: 0.366 AC: 774 AN: 2114

Alfa AF: 0.329 Hom.: 35184

Bravo AF: 0.399

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.67
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs11948993; hg19: chr5-8891510;