rs7898715

chr10-9572090-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_930643.2(LINC02663):n.715-38891C>T variant causes a intron, non coding transcript 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: LINC02663 XR_930643.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

Genes affected

LINC02663 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02663	XR_930643.2	n.715-38891C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.364

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7898715; hg19: chr10-9614053;