4-173840562-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.425

Alfa AF: 0.452 Hom.: 6629

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4695888; hg19: chr4-174761713;