rs7898715

Variant names:

• chr10-9572090-G-A
• rs7898715
• ENST00000796222.1:n.397-38891C>T

Variant summary

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

The ENST00000796222.1(ENSG00000303638):​n.397-38891C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,858 control chromosomes in the GnomAD database, including 11,061 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 0.36 (11061 hom., cov: 30)
• Consequence: ENSG00000303638 ENST00000796222.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 4 publications found

Genes affected

ENSG00000303638 (HGNC:):

LINC02663 (HGNC:54149): (long intergenic non-protein coding RNA 2663)

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 (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02663	XR_001747363.1	n.335-38891C>T		intron_variant	Intron 4 of 7
LINC02663	XR_930643.2	n.715-38891C>T		intron_variant	Intron 5 of 8
LINC02663	XR_930644.2	n.715-15221C>T		intron_variant	Intron 5 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303638	ENST00000796222.1	n.397-38891C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55086 AN: 151742 Hom.: 11057 Cov.: 30

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.363 AC: 55106 AN: 151858 Hom.: 11061 Cov.: 30 AF XY: 0.370 AC XY: 27432 AN XY: 74196

African (AFR) AF: 0.185 AC: 7672 AN: 41438

American (AMR) AF: 0.389 AC: 5927 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1306 AN: 3470

East Asian (EAS) AF: 0.485 AC: 2476 AN: 5106

South Asian (SAS) AF: 0.366 AC: 1758 AN: 4802

European-Finnish (FIN) AF: 0.551 AC: 5821 AN: 10560

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 28992 AN: 67914

Other (OTH) AF: 0.364 AC: 768 AN: 2112

Alfa AF: 0.399 Hom.: 2197

Bravo AF: 0.345

Asia WGS AF: 0.454 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.38
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs7898715; hg19: chr10-9614053;