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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796222.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000303638	ENST00000796222.1		n.397-41853C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10508393;

hg19: chr10-9617015;