rs17515642

Variant names:

• chr10-9526947-C-A
• rs17515642
• XR_001747363.1:n.475+6112G>T

Variant summary

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

The XR_001747363.1(LINC02663):​n.475+6112G>T variant causes a intron 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_001747363.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 2 publications found

Genes affected

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=-0.83).
• 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 rank	MANE	Protein	UniProt
LINC02663	XR_001747363.1	n.475+6112G>T		intron_variant	Intron 5 of 7
LINC02663	XR_930643.2	n.855+6112G>T		intron_variant	Intron 6 of 8
LINC02663	XR_930644.2	n.923+6112G>T		intron_variant	Intron 7 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0267 AC: 1110 AN: 41564

American (AMR) AF: 0.0796 AC: 1217 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3468

East Asian (EAS) AF: 0.0500 AC: 259 AN: 5176

South Asian (SAS) AF: 0.0541 AC: 261 AN: 4824

European-Finnish (FIN) AF: 0.251 AC: 2655 AN: 10588

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10845 AN: 68008

Other (OTH) AF: 0.105 AC: 223 AN: 2116

Alfa AF: 0.137 Hom.: 2336

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
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs17515642; hg19: chr10-9568910;