rs793108

Variant names:

• chr10-31126177-C-T
• rs793108
• ENST00000658872.1:n.510-17562C>T

Variant summary

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

The ENST00000658872.1(LINC02664):​n.510-17562C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,998 control chromosomes in the GnomAD database, including 14,352 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 0.40 (14352 hom., cov: 32)
• Consequence: LINC02664 ENST00000658872.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 43 publications found

Genes affected

LINC02664 (HGNC:54150): (long intergenic non-protein coding RNA 2664)

LOC105376481 (HGNC:):

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 = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376481	XR_001747410.3	n.2981+20052C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02664	ENST00000658872.1	n.510-17562C>T		intron_variant	Intron 2 of 2
LINC02664	ENST00000804994.1	n.277+20052C>T		intron_variant	Intron 2 of 3
LINC02664	ENST00000805304.1	n.399-17562C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61522 AN: 151878 Hom.: 14350 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.405 AC: 61529 AN: 151998 Hom.: 14352 Cov.: 32 AF XY: 0.410 AC XY: 30476 AN XY: 74302

African (AFR) AF: 0.167 AC: 6915 AN: 41484

American (AMR) AF: 0.523 AC: 7984 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1443 AN: 3466

East Asian (EAS) AF: 0.387 AC: 1995 AN: 5160

South Asian (SAS) AF: 0.376 AC: 1815 AN: 4822

European-Finnish (FIN) AF: 0.583 AC: 6148 AN: 10554

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33806 AN: 67934

Other (OTH) AF: 0.393 AC: 827 AN: 2106

Alfa AF: 0.463 Hom.: 35213

Bravo AF: 0.389

Asia WGS AF: 0.362 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.9
DANN	Benign	0.82
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs793108; hg19: chr10-31415106;