4-173840562-C-T

Variant names:

• chr4-173840562-C-T
• rs4695888
• ENST00000654333.1:n.318+6551C>T

Variant summary

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

The ENST00000654333.1(LINC02269):​n.318+6551C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,760 control chromosomes in the GnomAD database, including 15,166 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 0.43 (15166 hom., cov: 31)
• Consequence: LINC02269 ENST00000654333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 4 publications found

Genes affected

LINC02269 (HGNC:53184): (long intergenic non-protein coding RNA 2269)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 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
LINC02269	ENST00000654333.1	n.318+6551C>T		intron_variant	Intron 3 of 6
LINC02269	ENST00000654653.1	n.230-15722C>T		intron_variant	Intron 2 of 3
LINC02269	ENST00000654916.1	n.230-15722C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64720 AN: 151642 Hom.: 15165 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.427 AC: 64729 AN: 151760 Hom.: 15166 Cov.: 31 AF XY: 0.425 AC XY: 31509 AN XY: 74160

African (AFR) AF: 0.238 AC: 9867 AN: 41402

American (AMR) AF: 0.508 AC: 7729 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1532 AN: 3470

East Asian (EAS) AF: 0.671 AC: 3447 AN: 5140

South Asian (SAS) AF: 0.308 AC: 1482 AN: 4810

European-Finnish (FIN) AF: 0.435 AC: 4583 AN: 10544

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.507 AC: 34428 AN: 67878

Other (OTH) AF: 0.425 AC: 894 AN: 2102

Alfa AF: 0.456 Hom.: 7551

Bravo AF: 0.432

Asia WGS AF: 0.481 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.38
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs4695888; hg19: chr4-174761713;