rs7647526

chr3-180428809-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654328.1(LINC02053):n.264+14352T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,190 control chromosomes in the GnomAD database, including 1,847 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 0.10 (1847 hom., cov: 32)
• Consequence: LINC02053 ENST00000654328.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

Genes affected

LINC02053 (HGNC:52893): (long intergenic non-protein coding RNA 2053)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02053	ENST00000654328.1	n.264+14352T>G		intron_variant, non_coding_transcript_variant
LINC02053	ENST00000668671.1	n.282+14352T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15647 AN: 152072 Hom.: 1839 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0521

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.00620

Gnomad FIN AF: 0.00744

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0352

Gnomad OTH AF: 0.0822

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

GnomAD4 genome AF: 0.103 AC: 15688 AN: 152190 Hom.: 1847 Cov.: 32 AF XY: 0.0995 AC XY: 7407 AN XY: 74432

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.0518

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.00600

Gnomad4 FIN AF: 0.00744

Gnomad4 NFE AF: 0.0352

Gnomad4 OTH AF: 0.0833

Alfa AF: 0.0488 Hom.: 256

Bravo AF: 0.115

Asia WGS AF: 0.0220 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.7
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7647526; hg19: chr3-180146597;