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_930643.2(LINC02663):​n.855+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_930643.2 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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;