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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376481	XR_001747409.3	n.2795-15763C>T		intron_variant	Intron 1 of 2
LOC105376481	XR_001747410.3	n.2795-15763C>T		intron_variant	Intron 1 of 2
LOC105376481	XR_930796.3	n.904-15763C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02664	ENST00000658872.1	n.323-15763C>T		intron_variant	Intron 1 of 2
LINC02664	ENST00000804994.1	n.91-15763C>T		intron_variant	Intron 1 of 3
LINC02664	ENST00000805304.1	n.212-15763C>T		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs2793108; hg19: chr10-31379105;