rs3858304

chr10-130351311-A-Gchr10-130351311-A-T

Variant summary

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

The ENST00000648275.1(LINC02646):n.504-131570A>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 0.794 in 151,544 control chromosomes in the GnomAD database, including 47,654 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 0.79 (47654 hom., cov: 30)
• Consequence: LINC02646 ENST00000648275.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.800

Genes affected

LINC02646 (HGNC:54130): (long intergenic non-protein coding RNA 2646)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 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
LINC02646	ENST00000648275.1	n.504-131570A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120185 AN: 151422 Hom.: 47608 Cov.: 30

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.794 AC: 120287 AN: 151544 Hom.: 47654 Cov.: 30 AF XY: 0.794 AC XY: 58793 AN XY: 74020

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.791

Alfa AF: 0.766 Hom.: 35084

Bravo AF: 0.796

Asia WGS AF: 0.806 AC: 2800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.1
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3858304; hg19: chr10-132149575;