10-130258151-T-C

Position:

• chr10-130258151-T-C

Variant summary

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

The ENST00000648275.1(LINC02646):​n.503+44122T>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 0.892 in 152,276 control chromosomes in the GnomAD database, including 60,660 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 0.89 (60660 hom., cov: 33)
• Consequence: LINC02646 ENST00000648275.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 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.503+44122T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135749 AN: 152158 Hom.: 60618 Cov.: 33

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.892 AC: 135848 AN: 152276 Hom.: 60660 Cov.: 33 AF XY: 0.892 AC XY: 66431 AN XY: 74462

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.897

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.893

Alfa AF: 0.881 Hom.: 90033

Bravo AF: 0.889

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4751185; hg19: chr10-132056415;