6-108777824-C-T

Variant names:

• chr6-108777824-C-T
• rs1146229
• ENST00000720494.1:n.375-4364C>T

Variant summary

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

The ENST00000720494.1(LINC00222):​n.375-4364C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,762 control chromosomes in the GnomAD database, including 7,174 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 0.23 (7174 hom., cov: 31)
• Consequence: LINC00222 ENST00000720494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 1 publications found

Genes affected

LINC00222 (HGNC:21560): (long intergenic non-protein coding RNA 222)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 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
LINC00222	ENST00000720494.1	n.375-4364C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34625 AN: 151644 Hom.: 7134 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.229 AC: 34718 AN: 151762 Hom.: 7174 Cov.: 31 AF XY: 0.232 AC XY: 17222 AN XY: 74152

African (AFR) AF: 0.549 AC: 22664 AN: 41302

American (AMR) AF: 0.139 AC: 2124 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3472

East Asian (EAS) AF: 0.342 AC: 1762 AN: 5150

South Asian (SAS) AF: 0.259 AC: 1240 AN: 4796

European-Finnish (FIN) AF: 0.121 AC: 1273 AN: 10530

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.0707 AC: 4802 AN: 67948

Other (OTH) AF: 0.191 AC: 401 AN: 2104

Alfa AF: 0.125 Hom.: 8590

Bravo AF: 0.242

Asia WGS AF: 0.333 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.71
DANN	Benign	0.50
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1146229; hg19: chr6-109099027;