10-130258151-T-C

Variant names:

• chr10-130258151-T-C
• rs4751185
• ENST00000648275.1:n.503+44122T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648275.1(LINC02646):​n.503+44122T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 10 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02646	ENST00000648275.1	n.503+44122T>C		intron_variant	Intron 1 of 1
LINC02646	ENST00000739872.1	n.519+44122T>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.920 AC: 38236 AN: 41556

American (AMR) AF: 0.865 AC: 13231 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3074 AN: 3472

East Asian (EAS) AF: 0.898 AC: 4645 AN: 5174

South Asian (SAS) AF: 0.909 AC: 4387 AN: 4826

European-Finnish (FIN) AF: 0.897 AC: 9518 AN: 10610

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.879 AC: 59815 AN: 68022

Other (OTH) AF: 0.893 AC: 1885 AN: 2112

Alfa AF: 0.883 Hom.: 130096

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4751185; hg19: chr10-132056415;