chr10-130482151-C-A

Variant names:

• chr10-130482151-C-A
• rs381423
• ENST00000439421.2:n.24-730C>A

Variant summary

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

The ENST00000439421.2(LINC02646):​n.24-730C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0711 in 152,240 control chromosomes in the GnomAD database, including 1,086 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 0.071 (1086 hom., cov: 33)
• Consequence: LINC02646 ENST00000439421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 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
LINC02646	ENST00000439421.2	n.24-730C>A		intron_variant	Intron 1 of 1	3
LINC02646	ENST00000648275.1	n.504-730C>A		intron_variant	Intron 1 of 1
LINC02646	ENST00000657871.1	n.553-730C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0710 AC: 10808 AN: 152122 Hom.: 1085 Cov.: 33

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0273

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.00715

Gnomad OTH AF: 0.0588

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

GnomAD4 genome AF: 0.0711 AC: 10827 AN: 152240 Hom.: 1086 Cov.: 33 AF XY: 0.0692 AC XY: 5152 AN XY: 74434

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.0273

Gnomad4 ASJ AF: 0.0617

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0276

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.00715

Gnomad4 OTH AF: 0.0582

Alfa AF: 0.0000404 Hom.: 2099

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.049
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs381423; hg19: chr10-132280415;