10-130482151-C-T

Variant names:

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

Variant summary

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

The ENST00000439421.2(LINC02646):​n.24-730C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,224 control chromosomes in the GnomAD database, including 2,218 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 0.15 (2218 hom., cov: 33)
• Consequence: LINC02646 ENST00000439421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439421.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02646	ENST00000439421.2	TSL:3	n.24-730C>T		intron	N/A
	LINC02646	ENST00000648275.1		n.504-730C>T		intron	N/A
	LINC02646	ENST00000657871.1		n.553-730C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23118 AN: 152106 Hom.: 2210 Cov.: 33

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0989

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0909

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.152 AC: 23160 AN: 152224 Hom.: 2218 Cov.: 33 AF XY: 0.156 AC XY: 11596 AN XY: 74426

African (AFR) AF: 0.207 AC: 8604 AN: 41536

American (AMR) AF: 0.239 AC: 3652 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3470

East Asian (EAS) AF: 0.380 AC: 1964 AN: 5164

South Asian (SAS) AF: 0.186 AC: 897 AN: 4818

European-Finnish (FIN) AF: 0.0989 AC: 1050 AN: 10620

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0909 AC: 6181 AN: 68002

Other (OTH) AF: 0.150 AC: 317 AN: 2114

Alfa AF: 0.132 Hom.: 4149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.13
DANN	Benign	0.72
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs381423; hg19: chr10-132280415;