10-3241815-A-G

Variant names:

• chr10-3241815-A-G
• rs2764980
• ENST00000417149.2:n.981-1313T>C

Variant summary

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

The ENST00000417149.2(LINC02668):​n.981-1313T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,116 control chromosomes in the GnomAD database, including 17,624 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 0.47 (17624 hom., cov: 33)
• Consequence: LINC02668 ENST00000417149.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270
• Publications: 16 publications found

Genes affected

LINC02668 (HGNC:54154): (long intergenic non-protein coding RNA 2668)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417149.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02668	NR_187502.1		n.567+2752T>C		intron	N/A
	LINC02668	NR_187504.1		n.475-9233T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02668	ENST00000417149.2	TSL:3	n.981-1313T>C		intron	N/A
	LINC02668	ENST00000655354.1		n.633-1313T>C		intron	N/A
	LINC02668	ENST00000665182.1		n.633-1313T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70981 AN: 151998 Hom.: 17601 Cov.: 33

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.467 AC: 71042 AN: 152116 Hom.: 17624 Cov.: 33 AF XY: 0.480 AC XY: 35653 AN XY: 74352

African (AFR) AF: 0.309 AC: 12844 AN: 41502

American (AMR) AF: 0.568 AC: 8684 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1807 AN: 3466

East Asian (EAS) AF: 0.558 AC: 2883 AN: 5168

South Asian (SAS) AF: 0.550 AC: 2651 AN: 4822

European-Finnish (FIN) AF: 0.665 AC: 7036 AN: 10576

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33732 AN: 67986

Other (OTH) AF: 0.475 AC: 1004 AN: 2112

Alfa AF: 0.481 Hom.: 33731

Bravo AF: 0.454

Asia WGS AF: 0.558 AC: 1938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.19
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2764980; hg19: chr10-3284007;