10-2181819-T-C

Variant names:

• chr10-2181819-T-C
• rs10751855
• ENST00000418524.6:n.290-5387A>G

Variant summary

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

The ENST00000436003.4(LINC02662):​n.340-5387A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,050 control chromosomes in the GnomAD database, including 35,929 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 0.68 (35929 hom., cov: 32)
• Consequence: LINC02662 ENST00000436003.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 1 publications found

Genes affected

LINC02662 (HGNC:54148): (long intergenic non-protein coding RNA 2662)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436003.4. 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
	LINC02662	NR_184091.1		n.360-5387A>G		intron	N/A
	LINC02662	NR_184092.1		n.446+4693A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02662	ENST00000418524.6	TSL:5	n.290-5387A>G		intron	N/A
	LINC02662	ENST00000436003.4	TSL:3	n.340-5387A>G		intron	N/A
	LINC02662	ENST00000772890.1		n.411+4693A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103608 AN: 151932 Hom.: 35881 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.682 AC: 103711 AN: 152050 Hom.: 35929 Cov.: 32 AF XY: 0.687 AC XY: 51034 AN XY: 74318

African (AFR) AF: 0.618 AC: 25634 AN: 41466

American (AMR) AF: 0.779 AC: 11921 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2889 AN: 3470

East Asian (EAS) AF: 0.827 AC: 4273 AN: 5166

South Asian (SAS) AF: 0.900 AC: 4333 AN: 4816

European-Finnish (FIN) AF: 0.605 AC: 6388 AN: 10560

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45689 AN: 67964

Other (OTH) AF: 0.750 AC: 1581 AN: 2108

Alfa AF: 0.686 Hom.: 136023

Bravo AF: 0.692

Asia WGS AF: 0.860 AC: 2987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.35
PhyloP100		-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10751855;

hg19: chr10-2224013;