rs2793109

Variant names:

• chr10-31090917-T-A
• rs2793109
• ENST00000658872.1:n.323-15022T>A

Variant summary

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

The ENST00000658872.1(LINC02664):​n.323-15022T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,036 control chromosomes in the GnomAD database, including 14,214 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 (14214 hom., cov: 31)
• Consequence: LINC02664 ENST00000658872.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 8 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376481	XR_001747409.3	n.2795-15022T>A		intron_variant	Intron 1 of 2
LOC105376481	XR_001747410.3	n.2795-15022T>A		intron_variant	Intron 1 of 2
LOC105376481	XR_930796.3	n.904-15022T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02664	ENST00000658872.1	n.323-15022T>A		intron_variant	Intron 1 of 2
LINC02664	ENST00000804994.1	n.91-15022T>A		intron_variant	Intron 1 of 3
LINC02664	ENST00000805304.1	n.212-15022T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60976 AN: 151918 Hom.: 14214 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.401 AC: 60983 AN: 152036 Hom.: 14214 Cov.: 31 AF XY: 0.407 AC XY: 30221 AN XY: 74320

African (AFR) AF: 0.157 AC: 6518 AN: 41496

American (AMR) AF: 0.459 AC: 7011 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1393 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2044 AN: 5166

South Asian (SAS) AF: 0.363 AC: 1753 AN: 4826

European-Finnish (FIN) AF: 0.616 AC: 6508 AN: 10570

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34430 AN: 67924

Other (OTH) AF: 0.368 AC: 779 AN: 2114

Alfa AF: 0.461 Hom.: 2187

Bravo AF: 0.378

Asia WGS AF: 0.361 AC: 1255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.1
DANN	Benign	0.55
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs2793109; hg19: chr10-31379846;