rs17515642

chr10-9526947-C-A

Variant summary

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

The XR_930643.2(LINC02663):n.855+6112G>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 0.112 in 152,244 control chromosomes in the GnomAD database, including 1,307 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 0.11 (1307 hom., cov: 33)
• Consequence: LINC02663 XR_930643.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

Genes affected

LINC02663 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02663	XR_930643.2	n.855+6112G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17126 AN: 152126 Hom.: 1308 Cov.: 33

Gnomad AFR AF: 0.0268

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0797

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0501

Gnomad SAS AF: 0.0543

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.112 AC: 17122 AN: 152244 Hom.: 1307 Cov.: 33 AF XY: 0.114 AC XY: 8488 AN XY: 74414

Gnomad4 AFR AF: 0.0267

Gnomad4 AMR AF: 0.0796

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.0500

Gnomad4 SAS AF: 0.0541

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.105

Alfa AF: 0.132 Hom.: 196

Bravo AF: 0.0964

Asia WGS AF: 0.0650 AC: 226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.6
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17515642; hg19: chr10-9568910;