rs381423

Positions:

• chr10-130482151-C-A
• chr10-130482151-C-T

Variant summary

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

The ENST00000648275.1(LINC02646):​n.504-730C>A 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 0.0711 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 ENST00000648275.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02646	ENST00000648275.1	n.504-730C>A		intron_variant, non_coding_transcript_variant
LINC02646	ENST00000439421.2	n.24-730C>A		intron_variant, non_coding_transcript_variant		3
LINC02646	ENST00000657871.1	n.553-730C>A		intron_variant, non_coding_transcript_variant

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;