rs671330

chr6-152764099-A-Gchr6-152764099-A-T

Variant summary

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

The NR_183504.1(LINC02840):n.375-4015T>C 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 0.7 in 151,820 control chromosomes in the GnomAD database, including 37,589 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 0.70 (37589 hom., cov: 30)
• Consequence: LINC02840 NR_183504.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

Genes affected

LINC02840 (HGNC:54374): (long intergenic non-protein coding RNA 2840)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02840	NR_183504.1	n.375-4015T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02840	ENST00000666093.1	n.426-4015T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106110 AN: 151700 Hom.: 37547 Cov.: 30

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.676

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.700 AC: 106201 AN: 151820 Hom.: 37589 Cov.: 30 AF XY: 0.698 AC XY: 51796 AN XY: 74160

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.681

Alfa AF: 0.655 Hom.: 48116

Bravo AF: 0.703

Asia WGS AF: 0.720 AC: 2507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.35
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs671330; hg19: chr6-153085234;