chr10-3253481-G-A

Variant names:

• chr10-3253481-G-A
• rs4881131
• ENST00000417149.2:n.887+2979C>T

Variant summary

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

The ENST00000417149.2(LINC02668):​n.887+2979C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,056 control chromosomes in the GnomAD database, including 4,405 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 0.24 (4405 hom., cov: 32)
• Consequence: LINC02668 ENST00000417149.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657
• Publications: 2 publications found

Genes affected

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

LOC105376353 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.29 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.474+2979C>T		intron	N/A
	LINC02668	NR_187504.1		n.474+2979C>T		intron	N/A
	LINC02668	NR_187506.1		n.474+2979C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02668	ENST00000417149.2	TSL:3	n.887+2979C>T		intron	N/A
	LINC02668	ENST00000655354.1		n.539+2979C>T		intron	N/A
	LINC02668	ENST00000665182.1		n.539+2979C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35807 AN: 151938 Hom.: 4393 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.236 AC: 35857 AN: 152056 Hom.: 4405 Cov.: 32 AF XY: 0.242 AC XY: 17960 AN XY: 74310

African (AFR) AF: 0.165 AC: 6852 AN: 41496

American (AMR) AF: 0.284 AC: 4338 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 691 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1255 AN: 5168

South Asian (SAS) AF: 0.303 AC: 1459 AN: 4812

European-Finnish (FIN) AF: 0.321 AC: 3389 AN: 10544

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17082 AN: 67970

Other (OTH) AF: 0.235 AC: 495 AN: 2110

Alfa AF: 0.238 Hom.: 7472

Bravo AF: 0.228

Asia WGS AF: 0.311 AC: 1082 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.53
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs4881131; hg19: chr10-3295673;