rs2793108

Variant names:

• chr10-31090176-C-T
• rs2793108
• ENST00000658872.1:n.323-15763C>T

Variant summary

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

The ENST00000658872.1(LINC02664):​n.323-15763C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,878 control chromosomes in the GnomAD database, including 21,444 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 0.52 (21444 hom., cov: 31)
• Consequence: LINC02664 ENST00000658872.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 10 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658872.1. 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
	LINC02664	ENST00000658872.1		n.323-15763C>T		intron	N/A
	LINC02664	ENST00000804994.1		n.91-15763C>T		intron	N/A
	LINC02664	ENST00000805304.1		n.212-15763C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79148 AN: 151760 Hom.: 21426 Cov.: 31

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.522 AC: 79210 AN: 151878 Hom.: 21444 Cov.: 31 AF XY: 0.528 AC XY: 39173 AN XY: 74244

African (AFR) AF: 0.379 AC: 15684 AN: 41378

American (AMR) AF: 0.587 AC: 8954 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1763 AN: 3468

East Asian (EAS) AF: 0.500 AC: 2580 AN: 5160

South Asian (SAS) AF: 0.504 AC: 2428 AN: 4820

European-Finnish (FIN) AF: 0.692 AC: 7308 AN: 10566

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.572 AC: 38844 AN: 67914

Other (OTH) AF: 0.490 AC: 1032 AN: 2106

Alfa AF: 0.551 Hom.: 73641

Bravo AF: 0.507

Asia WGS AF: 0.500 AC: 1738 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	0.19
DANN	Benign	0.39
PhyloP100		-1.4

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: rs2793108;

hg19: chr10-31379105;