10-130258151-T-C

Variant names:

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

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 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

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;