rs10508393

Variant names:

• chr10-9575052-G-A
• rs10508393
• ENST00000796222.1:n.397-41853C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-9575052-G-A
• chr10-9575052-G-C
• chr10-9575052-G-T

Variant summary

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

The ENST00000796222.1(ENSG00000303638):​n.397-41853C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,978 control chromosomes in the GnomAD database, including 3,307 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 0.20 (3307 hom., cov: 32)
• Consequence: ENSG00000303638 ENST00000796222.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510
• 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=-0.52).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02663	XR_001747363.1	n.335-41853C>T		intron_variant	Intron 4 of 7
LINC02663	XR_930643.2	n.715-41853C>T		intron_variant	Intron 5 of 8
LINC02663	XR_930644.2	n.715-18183C>T		intron_variant	Intron 5 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303638	ENST00000796222.1	n.397-41853C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30122 AN: 151860 Hom.: 3302 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.198 AC: 30166 AN: 151978 Hom.: 3307 Cov.: 32 AF XY: 0.197 AC XY: 14630 AN XY: 74256

African (AFR) AF: 0.273 AC: 11329 AN: 41444

American (AMR) AF: 0.225 AC: 3426 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3470

East Asian (EAS) AF: 0.0215 AC: 111 AN: 5170

South Asian (SAS) AF: 0.276 AC: 1326 AN: 4810

European-Finnish (FIN) AF: 0.122 AC: 1290 AN: 10560

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11392 AN: 67958

Other (OTH) AF: 0.199 AC: 421 AN: 2112

Alfa AF: 0.179 Hom.: 10989

Bravo AF: 0.207

Asia WGS AF: 0.163 AC: 568 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	8.5
DANN	Benign	0.63
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs10508393; hg19: chr10-9617015;