10-3936343-A-T

Position:

• chr10-3936343-A-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02660	ENST00000692986.1	n.167-4868A>T		intron_variant, non_coding_transcript_variant

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;