10-3936343-A-T

Variant names:

• chr10-3936343-A-T
• rs10508270
• ENST00000692986.1:n.167-4868A>T

Variant summary

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

The ENST00000692986.1(LINC02660):​n.167-4868A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0097 in 152,290 control chromosomes in the GnomAD database, including 38 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 0.0097 (38 hom., cov: 32)
• Consequence: LINC02660 ENST00000692986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.554

Genes affected

LINC02660 (HGNC:54146): (long intergenic non-protein coding RNA 2660)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02660	ENST00000692986.1	n.167-4868A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.00973 AC: 1480 AN: 152172 Hom.: 38 Cov.: 32

Gnomad AFR AF: 0.00167

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.0221

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00168

Gnomad OTH AF: 0.0129

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

GnomAD4 genome AF: 0.00970 AC: 1477 AN: 152290 Hom.: 38 Cov.: 32 AF XY: 0.0113 AC XY: 838 AN XY: 74472

Gnomad4 AFR AF: 0.00166

Gnomad4 AMR AF: 0.0579

Gnomad4 ASJ AF: 0.00346

Gnomad4 EAS AF: 0.0220

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.0137

Gnomad4 NFE AF: 0.00168

Gnomad4 OTH AF: 0.0133

Alfa AF: 0.00364 Hom.: 1

Bravo AF: 0.0144

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508270; hg19: chr10-3978535;